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Table 1 Summary statistics of differential SNPs and their corresponding genes identified by RAD sequencing

From: Physical mapping of QTL for tuber yield, starch content and starch yield in tetraploid potato (Solanum tuberosum L.) by means of genome wide genotyping by sequencing and the 8.3 K SolCAP SNP array

Data filtering criteria Total No. TSC TY TSY TSC and TY TSC and TSY TY and TSY TSC, TY and TSY
1. Total No. of SNPs nd 579,352 601,837 598,703 nd nd nd nd
2. No. of SNPs with differential allele frequency (FDR < 0.05) nd 58,850 46,542 20,402 nd nd nd nd
3. No. of SNPs with differential allele frequency in annotated genes (FDR < 0.05) 25,501 10,986 5660 2207 3005 665 2330 648
4. No. of annotated genes with differential SNPs (FDR < 0.05) 6664 1456 654 218 1575 430 532 1799
5. No. of SNPs with differential allele frequency in annotated genes causing amino acid changes (FDR < 0.05) 4668 1993 1043 403 537 135 433 124
6. No. of annotated genes with differential SNPs causing amino acid changes (FDR < 0.05) 2308 378 146 43 622 162 168 789
7. No. of SNPs with differential allele frequency in annotated genes causing amino acid changes (FDR < 0.0001) 582 310 148 58 40 1 23 2
8. No. of annotated genes with at least one differential SNP with FDR < 0.001 3144 431 81 13 842 194 257 1326
  1. nd not determined
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BMC Genomics

ISSN: 1471-2164

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