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== Check SNP == *In the SNP file from bisReadMapperSE19Triton mapping (1) chromosome name (2) position (3) reference base call (4) strand (Watson/Crick) (5) variant call (6) variant quality (7) total read depth (8,10,12..etc) depth of sequenced base (9,11,13..etc) base sequenced * SNPs before filtered chr12 '''25537917''' A C A 157 44 A 44 chr16 '''84539303''' C C K 49 21 T 6 G 15 chr2 '''44588941''' G W R 94 31 A 16 G 15 * SNP after filtered 19,781 GK0005-001.fwd.pileup.snp.filtered head 3 GK0005-001.fwd.pileup.snp.filtered SNP position SNP call SNP qual dbSNP RefAlleles SNP call(fwd) Allele count(fwd) SNP call(rev) Allele count(rev) '''chr12:25537917''' T 157 rs923491 K - - A A,44 '''chr16:84539303''' S 49 rs12716753 S - - K T,6,G,15 '''chr2:44588941''' R 94 rs698775 R R A,16,G,15 - - * SNP called by Robert's pipeline 18,146 SNPs.GK0005001.txt chr12 '''25537917''' A AA homozygous - ss chr16 '''84539303''' CG TG heterozygous - ss chr2 '''44588941''' AG AG heterozygous + ss * SNPDB Assembly Genome_Build Chr Chr_Pos rs923491 --> GRCh37.p5 37.3 12 25537917 RefSNP Alleles: G/T (check) rs12716753 --> GRCh37.p5 37.3 16 84539303 RefSNP Alleles: C/G rs698775 --> GRCh37.p5 37.3 2 44588941 RefSNP Alleles: A/G * The results above revealed that the SNP called by both methods were consistent
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