-- dump date   	20240506_053128
-- class       	Genbank::Contig
-- table       	contig_comment
-- id	comment
NZ_CP022297.1	REFSEQ INFORMATION: The reference sequence is identical toREFSEQ INFORMATION: The reference sequence is identical to CP022297.1.REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of EnvironmentalREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University ofREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657.REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmedREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, usingREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher forREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and aREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fitsREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determinedREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copiesREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exactREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing theREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that isREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected byREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is usedREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distanceREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled repliconREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detectingREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in theREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finishedREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributionsREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was alsoREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our finalREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. andREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, lengthREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded asREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# ofREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings.REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome AnnotationREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here:REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter.REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START##REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the MarineREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading BacteriumREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: FullREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: YesREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0xREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeqREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END##REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START##REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeqREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic GenomeREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP)REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference proteinREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNAREFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90 rRNAs                             :: 5, 5, 5 (5S, 16S, 23S)REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90 rRNAs                             :: 5, 5, 5 (5S, 16S, 23S) complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S)REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90 rRNAs                             :: 5, 5, 5 (5S, 16S, 23S) complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S) tRNAs                             :: 69REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90 rRNAs                             :: 5, 5, 5 (5S, 16S, 23S) complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S) tRNAs                             :: 69 ncRNAs                            :: 6REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90 rRNAs                             :: 5, 5, 5 (5S, 16S, 23S) complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S) tRNAs                             :: 69 ncRNAs                            :: 6 Pseudo Genes (total)              :: 37REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90 rRNAs                             :: 5, 5, 5 (5S, 16S, 23S) complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S) tRNAs                             :: 69 ncRNAs                            :: 6 Pseudo Genes (total)              :: 37 CDSs (without protein)            :: 37REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90 rRNAs                             :: 5, 5, 5 (5S, 16S, 23S) complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S) tRNAs                             :: 69 ncRNAs                            :: 6 Pseudo Genes (total)              :: 37 CDSs (without protein)            :: 37 Pseudo Genes (ambiguous residues) :: 0 of 37REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90 rRNAs                             :: 5, 5, 5 (5S, 16S, 23S) complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S) tRNAs                             :: 69 ncRNAs                            :: 6 Pseudo Genes (total)              :: 37 CDSs (without protein)            :: 37 Pseudo Genes (ambiguous residues) :: 0 of 37 Pseudo Genes (frameshifted)       :: 10 of 37REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90 rRNAs                             :: 5, 5, 5 (5S, 16S, 23S) complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S) tRNAs                             :: 69 ncRNAs                            :: 6 Pseudo Genes (total)              :: 37 CDSs (without protein)            :: 37 Pseudo Genes (ambiguous residues) :: 0 of 37 Pseudo Genes (frameshifted)       :: 10 of 37 Pseudo Genes (incomplete)         :: 30 of 37REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90 rRNAs                             :: 5, 5, 5 (5S, 16S, 23S) complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S) tRNAs                             :: 69 ncRNAs                            :: 6 Pseudo Genes (total)              :: 37 CDSs (without protein)            :: 37 Pseudo Genes (ambiguous residues) :: 0 of 37 Pseudo Genes (frameshifted)       :: 10 of 37 Pseudo Genes (incomplete)         :: 30 of 37 Pseudo Genes (internal stop)      :: 9 of 37REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90 rRNAs                             :: 5, 5, 5 (5S, 16S, 23S) complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S) tRNAs                             :: 69 ncRNAs                            :: 6 Pseudo Genes (total)              :: 37 CDSs (without protein)            :: 37 Pseudo Genes (ambiguous residues) :: 0 of 37 Pseudo Genes (frameshifted)       :: 10 of 37 Pseudo Genes (incomplete)         :: 30 of 37 Pseudo Genes (internal stop)      :: 9 of 37 Pseudo Genes (multiple problems)  :: 9 of 37REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90 rRNAs                             :: 5, 5, 5 (5S, 16S, 23S) complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S) tRNAs                             :: 69 ncRNAs                            :: 6 Pseudo Genes (total)              :: 37 CDSs (without protein)            :: 37 Pseudo Genes (ambiguous residues) :: 0 of 37 Pseudo Genes (frameshifted)       :: 10 of 37 Pseudo Genes (incomplete)         :: 30 of 37 Pseudo Genes (internal stop)      :: 9 of 37 Pseudo Genes (multiple problems)  :: 9 of 37 CRISPR Arrays                     :: 5REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90 rRNAs                             :: 5, 5, 5 (5S, 16S, 23S) complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S) tRNAs                             :: 69 ncRNAs                            :: 6 Pseudo Genes (total)              :: 37 CDSs (without protein)            :: 37 Pseudo Genes (ambiguous residues) :: 0 of 37 Pseudo Genes (frameshifted)       :: 10 of 37 Pseudo Genes (incomplete)         :: 30 of 37 Pseudo Genes (internal stop)      :: 9 of 37 Pseudo Genes (multiple problems)  :: 9 of 37 CRISPR Arrays                     :: 5 ##Genome-Annotation-Data-END##REFSEQ INFORMATION: The reference sequence is identical to CP022297.1. Bacteria and source DNA available from Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657. The adjacency of the scaffold ends (absence of a gap) was confirmed by inspecting the ace file, a Newbler output file, using AceFileViewer software. Gaps were examined with GenoFinisher for the identification of repeat-induced gaps (pseudogaps), and a repeat contig or a sequence of repeat contigs that reasonably fits each gap were identified. The sequence of the gaps was determined by AceFileViewer, which detects nucleotide variations among copies of a repeat contig and determines the context-dependent exact sequence. AceFileViewer uses mate-pair reads, one containing the nucleotide variation and the other belonging to a contig that is neighboring to the gap. In cases where false gaps are detected by finding gap-flanking overlapping contig ends, AceFileViewer is used to verify if the overlap is supported by the pair-distance distribution of reads that flank the gap. Assembled replicon sequences were confirmed using FinishChecker by (i) detecting 21-mers that are absent in the Illumina reads but present in the finished sequences and (ii) by mapping mate-pairs to the finished sequences and searching for abnormal distance distributions (z-test).  Biased distribution of singly-mapped mate-pairs was also checked. Those checking schemes confirmed the accuracy of our final assemblies. Except for Newbler (overlapMinMatchIdentity. and allContigThresh=0) and ShortReadManger (score threshold0, length threshold!, and 21-mers occurring more than twice were regarded as valid), AceFileViewer, GenoFinisher, and #findmate# of ShortReadManager were run under default settings. The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ Annotation modified by submitter. ##Genome-Assembly-Data-START## Assembly Date          :: MAR-2017 Assembly Method        :: Newbler v. 2.8; GenoFinisher v. 2.0;                           AceFileViewer v. 1.4 Assembly Name          :: Complete Genome Sequence of the Marine                           Carbazole-Degrading Bacterium                           Marinobacterium georgiense IC961 Genome Representation  :: Full Expected Final Version :: Yes Genome Coverage        :: 81.0x Sequencing Technology  :: Illumina MiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider               :: NCBI RefSeq Annotation Name                   :: GCF_017310015.1-RS_2024_04_22 Annotation Date                   :: 04/22/2024 04:05:28 Annotation Pipeline               :: NCBI Prokaryotic Genome                                      Annotation Pipeline (PGAP) Annotation Method                 :: Best-placed reference protein                                      set; GeneMarkS-2+ Annotation Software revision      :: 6.7 Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA Genes (total)                     :: 3,827 CDSs (total)                      :: 3,737 Genes (coding)                    :: 3,700 CDSs (with protein)               :: 3,700 Genes (RNA)                       :: 90 rRNAs                             :: 5, 5, 5 (5S, 16S, 23S) complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S) tRNAs                             :: 69 ncRNAs                            :: 6 Pseudo Genes (total)              :: 37 CDSs (without protein)            :: 37 Pseudo Genes (ambiguous residues) :: 0 of 37 Pseudo Genes (frameshifted)       :: 10 of 37 Pseudo Genes (incomplete)         :: 30 of 37 Pseudo Genes (internal stop)      :: 9 of 37 Pseudo Genes (multiple problems)  :: 9 of 37 CRISPR Arrays                     :: 5 ##Genome-Annotation-Data-END## COMPLETENESS: full length.