; variation-scan -v 2 -m_format transfac -m $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -i public_html/demo_files/variation_demo_set_MWeirauch_cell_2014_15SNPs.var-seq -bg $RSAT/public_html/data/genomes/Homo_sapiens_GRCh37/oligo-frequencies/3nt_upstream-noorf_Homo_sapiens_GRCh37-ovlp-1str.freq.gz -lth score 1 -lth w_diff 1 -lth pval_ratio 10 -uth pval 0.001 -o results/variation_scan_demo/varscan_weirauch-snps_vs_JASPAR_pval000.1_pvalratio10.tab ; Program version 1.15 ; Input files ; bg /no_backup/rsat/public_html/data/genomes/Homo_sapiens_GRCh37/oligo-frequencies/3nt_upstream-noorf_Homo_sapiens_GRCh37-ovlp-1str.freq.gz ; input public_html/demo_files/variation_demo_set_MWeirauch_cell_2014_15SNPs.var-seq ; distrib_list ; Output files ; output results/variation_scan_demo/varscan_weirauch-snps_vs_JASPAR_pval0.1_pvalratio2.tab ; column content ; 1 matrix_ac Accession number of the positions-pecific scoring matrix ; 2 matrix_name Name of the matrix (generally the transcription factor name) ; 3 var_id ID of the variation ; 4 var_class Variation type, according to SNP Ontology (SO) nomenclature ; 5 var_coord Coordinates of the variation ; 6 best_w Best weigth for the putative site ; 7 worst_w Worst weigth for the putative site ; 8 w_diff Difference between best and worst weigth ; 9 best_pval P_value of the best putative site ; 10 worst_pval P_value of the worst putative site ; 11 pval_ratio Ratio between worst and best pval ( pval_ratio = worst_pval/best_pval ) ; 12 best_variant Variant in the best putative site ; 13 worst_variant Variant in the worst putative site ; 14 best_offest Offset of the best putative site ; 15 worst_offset Offset of the worst putative site ; 16 min_offset_diff Difference minimal between best and worst putative site ; 17 best_strand Strand of the best putative site ; 18 worst_strand Strand of the worst putative site ; 19 str_change Indicate if strand have change between the offset of min_offset_diff ; 20 best_seq Sequence of the worst putative site ; 21 worst_seq Sequence of the worst putative site ; 22 reference_allele Reference allele ; 23 is_ref_better Flag if the reference allele is the allele with the best score ; 24 monir_alle_freq Minor allele frequency #ac_motif motif var_id var_class var_coord best_w worst_w w_diff best_pval worst_pval pval_ratio best_variant worst_variant best_offset worst_offset min_offset_diff best_strand worst_strand str_change best_seq worst_seq reference_allele is_ref_better minor_allele_freq MA0019.1 Ddit3::Cebpa rs7895676 SNV 10:123333997-123333997_+ 6.6 2.7 3.90 1.8e-04 2.7e-03 15.00 T C -5 -5 0 R R 0 TGGTGCAATCTG TGGTGCGATCTG C N 0.376033 MA0025.1 NFIL3 rs11986220 SNV 8:128531689-128531689_+ 4.8 -0.0 4.80 4.4e-04 6.3e-03 14.32 T A -3 -3 0 R R 0 TTATTTAATTT TTATTTATTTT A N 0.103765 MA0028.1 ELK1 rs554219 SNV 11:69331642-69331642_+ 7.1 4.3 2.80 1.5e-04 1.8e-03 12.00 C G -4 -4 0 D D 0 TCACCGGAAA TCACGGGAAA C Y 0.114325 MA0030.1 FOXF2 rs1859961 SNV 17:69108655-69108655_+ 3.6 -1.1 4.70 7.9e-04 8.3e-03 10.51 A G -11 -11 0 D D 0 GGAAGGCAAATAAC GGAAGGCAAATGAC A Y 0.00367309 MA0041.1 Foxd3 rs11986220 SNV 8:128531689-128531689_+ 6.2 1.4 4.80 2.8e-04 5.2e-03 18.57 A T -6 -6 0 R R 0 ATTTATTTTTTT ATTTAATTTTTT A Y 0.103765 MA0042.1 FOXI1 rs11986220 SNV 8:128531689-128531689_+ 7.5 3.4 4.10 1.2e-04 1.7e-03 14.17 A T -2 -2 0 R R 0 TTTTATTTATTT TTTTATTTAATT A Y 0.103765 MA0043.1 HLF rs12740374 SNV 1:109817590-109817590_+ 5.9 1.0 4.90 3.2e-04 9.8e-03 30.62 T G -2 -2 0 D D 0 GGTTGCTCAATC GGGTGCTCAATC G N 0.18641 MA0063.1 Nkx2-5 rs4784227 SNV 16:52599188-52599188_+ 6.8 3.8 3.00 1.7e-04 4.2e-03 24.71 C T 0 0 0 R R 0 ATAATCG ATAATCA C Y 0.21809 MA0067.1 Pax2 rs6983267 SNV 8:128413305-128413305_+ 5.9 0.8 5.10 3.8e-04 3.4e-02 89.47 T G -2 -2 0 D D 0 AGTCACTG AGGCACTG G N 0.436639 MA0071.1 RORA_1 rs6983267 SNV 8:128413305-128413305_+ 5.1 -0.0 5.10 4.4e-04 7.6e-03 17.27 T G -7 -7 0 D D 0 ATGAAAGTCA ATGAAAGGCA G N 0.436639 MA0081.1 SPIB rs57095329 SNV 5:159894847-159894847_+ 6.4 1.6 4.80 5.7e-04 1.1e-02 19.30 A G 0 0 0 D D 0 ACAGGAA GCAGGAA A Y 0.117539 MA0132.1 Pdx1 rs11986220 SNV 8:128531689-128531689_+ 5.7 0.4 5.30 1.0e-03 2.2e-02 22.00 T A -2 -2 0 R R 0 TTAATT TTATTT A N 0.103765 MA0135.1 Lhx3 rs11986220 SNV 8:128531689-128531689_+ 6.8 2.1 4.70 1.1e-04 2.1e-03 19.09 T A -3 -3 0 D D 0 AAATTAAATAAAA AAAATAAATAAAA A N 0.103765 MA0135.1 Lhx3 rs11986220 SNV 8:128531689-128531689_+ 6.3 1.5 4.80 1.5e-04 2.8e-03 18.67 T A -6 -6 0 R R 0 TATTTAATTTTTT TATTTATTTTTTT A N 0.103765 MA0062.2 GABPA rs554219 SNV 11:69331642-69331642_+ 6.4 1.1 5.30 1.4e-04 1.6e-03 11.43 C G -1 -1 0 D D 0 CCGGAAACCCA CGGGAAACCCA C Y 0.114325 MA0039.2 Klf4 rs1542725 SNV 4:145488334-145488334_+ 5.0 0.2 4.80 5.1e-04 6.1e-03 11.96 C T -4 -4 0 R R 0 TGGGAGGGGA TGGGAAGGGA C Y 0.294307 MA0002.2 RUNX1 rs2981578 SNV 10:123340311-123340311_+ 5.5 -4.3 9.80 6.3e-04 7.1e-02 112.70 C T -4 -4 0 R R 0 ATATGCGGTTT ATATGCAGTTT C Y 0.37787 MA0047.2 Foxa2 rs1859961 SNV 17:69108655-69108655_+ 3.8 -2.7 6.50 7.6e-04 1.2e-02 15.79 A G -11 -11 0 R R 0 TATTTGCCTTCC CATTTGCCTTCC A Y 0.00367309 MA0151.1 ARID3A rs11986220 SNV 8:128531689-128531689_+ 6.9 2.1 4.80 4.1e-04 7.1e-03 17.32 T A -1 -1 0 D D 0 ATTAAA AATAAA A N 0.103765 MA0158.1 HOXA5 rs2981578 SNV 10:123340311-123340311_+ 5.5 0.9 4.60 9.0e-04 2.3e-02 25.56 C T 0 0 0 D D 0 CGCATATT TGCATATT C Y 0.37787 MA0463.1 Bcl6 SNP195 SNV 16:209709-209709_+ 4.6 -4.0 8.60 5.9e-04 2.1e-02 35.59 T C -5 -5 0 D D 0 ATTATTAGAAAATA ATTATCAGAAAATA T Y NA MA0466.1 CEBPB rs7895676 SNV 10:123333997-123333997_+ 11.0 -0.7 11.70 2.5e-06 6.1e-04 244.00 T C -3 -3 0 D D 0 GATTGCACCAC GATCGCACCAC C N 0.376033 MA0466.1 CEBPB rs12740374 SNV 1:109817590-109817590_+ 8.4 -5.1 13.50 3.9e-05 1.7e-03 43.59 T G -2 -2 0 D D 0 GGTTGCTCAAT GGGTGCTCAAT G N 0.18641 MA0471.1 E2F6 rs57095329 SNV 5:159894847-159894847_+ 3.8 -5.3 9.10 5.0e-04 7.4e-03 14.80 G A -2 -2 0 D D 0 AGGCAGGAAGC AGACAGGAAGC A N 0.117539 MA0473.1 ELF1 rs554219 SNV 11:69331642-69331642_+ 2.6 -7.1 9.70 6.9e-04 7.6e-03 11.01 C G -5 -5 0 D D 0 CTCACCGGAAACC CTCACGGGAAACC C Y 0.114325 MA0475.1 FLI1 rs554219 SNV 11:69331642-69331642_+ 5.6 -2.5 8.10 3.2e-04 3.5e-03 10.94 C G -2 -2 0 D D 0 ACCGGAAACCC ACGGGAAACCC C Y 0.114325 MA0481.1 FOXP1 rs11986220 SNV 8:128531689-128531689_+ 6.2 0.9 5.30 2.0e-04 2.8e-03 14.00 A T -5 -5 0 D D 0 AAAAAATAAATAAAA AAAAATTAAATAAAA A Y 0.103765 MA0482.1 Gata4 rs8072254 SNV 17:69107816-69107816_+ 2.5 -6.9 9.40 6.8e-04 1.1e-02 16.18 A G -7 -7 0 R R 0 GGTTCTCACCG GGTCCTCACCG A Y 0.353076 MA0483.1 Gfi1b rs12740374 SNV 1:109817590-109817590_+ 4.1 -5.5 9.60 6.4e-04 1.3e-02 20.31 T G -8 -8 0 R R 0 CAACCTCAGGG CACCCTCAGGG G N 0.18641 MA0493.1 Klf1 rs1542725 SNV 4:145488334-145488334_+ 4.3 -2.9 7.20 5.5e-04 7.8e-03 14.18 C T -5 -5 0 D D 0 GTCCCCTCCCA GTCCCTTCCCA C Y 0.294307 MA0494.1 Nr1h3::Rxra rs12740374 SNV 1:109817590-109817590_+ 5.7 -0.5 6.20 2.4e-04 7.2e-03 30.00 T G -10 -10 0 D D 0 TGCCCTGAGGTTGCTCAAT TGCCCTGAGGGTGCTCAAT G N 0.18641 MA0495.1 MAFF rs4784227 SNV 16:52599188-52599188_+ 7.7 -3.4 11.10 6.2e-05 1.1e-02 177.42 T C -9 -9 0 R R 0 CAATAATCAGCAAACACT CAATAATCGGCAAACACT C N 0.21809 MA0496.1 MAFK rs4784227 SNV 16:52599188-52599188_+ 8.2 -3.1 11.30 4.9e-05 4.2e-03 85.71 T C -7 -7 0 R R 0 AATAATCAGCAAACA AATAATCGGCAAACA C N 0.21809 MA0506.1 NRF1 rs35054928 deletion 10:123340432-123340432_+ 9.2 -4.3 13.50 1.4e-05 4.6e-03 328.57 C -4 -9 -5 R D 1 GAGCCGGCGCA GGCTGTGCGCG,GGAGCCGCGCA C Y 0.485767 MA0527.1 ZBTB33 rs554219 SNV 11:69331642-69331642_+ 5.8 -2.4 8.20 1.1e-04 4.5e-03 40.91 G C -10 -10 0 R R 0 TTCCCGTGAGGATTT TTCCGGTGAGGATTT C N 0.114325 MA0527.1 ZBTB33 rs554219 SNV 11:69331642-69331642_+ 2.7 -5.5 8.20 5.4e-04 1.3e-02 24.07 G C -7 -7 0 D D 0 TCCTCACGGGAAACC TCCTCACCGGAAACC C N 0.114325 MA0102.3 CEBPA rs7895676 SNV 10:123333997-123333997_+ 9.5 -0.4 9.90 1.5e-05 6.9e-04 46.00 T C -2 -2 0 D D 0 ATTGCACCACT ATCGCACCACT C N 0.376033 MA0102.3 CEBPA rs12740374 SNV 1:109817590-109817590_+ 8.6 -2.9 11.50 3.8e-05 1.6e-03 42.11 T G -1 -1 0 D D 0 GTTGCTCAATC GGTGCTCAATC G N 0.18641 MA0076.2 ELK4 rs554219 SNV 11:69331642-69331642_+ 8.1 -1.1 9.20 5.1e-05 2.2e-03 43.14 C G -2 -2 0 R R 0 GGGTTTCCGGT GGGTTTCCCGT C Y 0.114325 MA0148.3 FOXA1 rs1859961 SNV 17:69108655-69108655_+ 6.4 -4.9 11.30 1.7e-04 5.0e-03 29.41 A G -10 -10 0 R R 0 TTGTTATTTGCCTTC TTGTCATTTGCCTTC A Y 0.00367309 MA0100.2 Myb rs2981578 SNV 10:123340311-123340311_+ 5.5 -2.0 7.50 2.9e-04 3.9e-03 13.45 T C -5 -5 0 D D 0 CAAACTGCAT CAAACCGCAT C N 0.37787 MA0105.3 NFKB1 rs554219 SNV 11:69331642-69331642_+ 6.7 -3.4 10.10 1.6e-04 8.6e-03 53.75 G C -1 -1 0 R R 0 TGGGTTTCCCG TGGGTTTCCGG C N 0.114325 MA0014.2 PAX5 rs75915166 SNV 11:69379161-69379161_+ 7.9 2.6 5.30 3.8e-05 1.3e-03 34.21 C A -13 -13 0 D D 0 GAGATCATCCAGGCTTAAC GAGATCATCCAGGATTAAC C Y 0.0284665 MA0137.3 STAT1 rs554219 SNV 11:69331642-69331642_+ 2.5 -6.5 9.00 8.1e-04 1.3e-02 16.05 G C -5 -5 0 D D 0 CTCACGGGAAA CTCACCGGAAA C N 0.114325 MA0137.3 STAT1 SNP195 SNV 16:209709-209709_+ 2.7 -4.6 7.30 7.5e-04 7.8e-03 10.40 T C -5 -5 0 D D 0 ATTATTAGAAA ATTATCAGAAA T Y NA MA0144.2 STAT3 rs554219 SNV 11:69331642-69331642_+ 4.1 -6.9 11.00 8.5e-04 1.5e-02 17.65 G C -5 -5 0 D D 0 CTCACGGGAAA CTCACCGGAAA C N 0.114325 MA0140.2 TAL1::GATA1 SNP195 SNV 16:209709-209709_+ 10.1 0.5 9.60 8.2e-06 1.1e-03 134.15 C T -5 -5 0 D D 0 ATTATCAGAAAATAACAG ATTATTAGAAAATAACAG T N NA MA0003.2 TFAP2A rs12740374 SNV 1:109817590-109817590_+ 9.6 7.2 2.40 9.6e-06 1.3e-04 13.54 G T -10 -10 0 R R 0 AGCACCCTCAGGGCA AGCAACCTCAGGGCA G Y 0.18641 MA0093.2 USF1 rs1859961 SNV 17:69108655-69108655_+ 2.8 -8.3 11.10 7.3e-04 1.3e-02 17.81 G A -7 -7 0 D D 0 GGCAAATGACA GGCAAATAACA A N 0.00367309 MA0594.1 Hoxa9 rs11986220 SNV 8:128531689-128531689_+ 3.7 -2.3 6.00 7.4e-04 1.1e-02 14.86 A T -3 -3 0 D D 0 AAAATAAATAA AAATTAAATAA A Y 0.103765 MA0595.1 SREBF1 rs7895676 SNV 10:123333997-123333997_+ 5.1 -1.4 6.50 3.4e-04 7.5e-03 22.06 C T -2 -2 0 D D 0 ATCGCACCAC ATTGCACCAC C Y 0.376033 MA0596.1 SREBF2 rs7895676 SNV 10:123333997-123333997_+ 5.4 -0.9 6.30 3.2e-04 7.6e-03 23.75 C T -2 -2 0 R R 0 GTGGTGCGAT GTGGTGCAAT C Y 0.376033 MA0599.1 KLF5 rs1542725 SNV 4:145488334-145488334_+ 7.7 -2.7 10.40 1.1e-04 2.7e-03 24.55 C T -4 -4 0 D D 0 TCCCCTCCCA TCCCTTCCCA C Y 0.294307 ; Total variations scan 15 ; Total sequences scan 6150 ; Total matrices 205 ; Host name caminante.local ; Job started 2015-03-25.180454 ; Job done 2015-03-25.181821 ; Seconds 6.12 ; user 6.12 ; system 0.87 ; cuser 791.79 ; csystem 8.77