Additional file 3: Table S1. of DiSNPindel: improved intra-individual SNP and InDel detection in direct amplicon sequencing of a diploid

Found and missed SNPs out of the 66 CAPS-associated intra-individual SNPs from 62 single traces [22] by four software packages DiSNPindel, novoSNP [8], Mutation Surveyor ( http://www.softgenetics.com/mutationSurveyor.html ) and PolyPhred [6, 9]. Table S2. True, false positive and missed SNPs by four software packages DiSNPindel, novoSNP [8], Mutation Surveyor ( http://www.softgenetics.com/mutationSurveyor.html ) and PolyPhred [6, 9] for 50 amplicons previously directly sequenced [22]. Those sequencing traces with no detection results shown in novoSNP and/or unmatched with reference sequence in Mutation Surveyor were excluded. Table S3. InDels detected by four software packages DiSNPindel, novoSNP [8], Mutation Surveyor ( http://www.softgenetics.com/mutationSurveyor.html ), PolyPhred [6, 9] and PrimeIndel [10] for 77 previously directly sequenced amplicons that contained within-individual variation in simple sequence repeats [23]. (XLS 399Â kb)