Sequencing platform(DNA source)(a) | SNPs | SNPs % | Number of reference sequences with SNPs (AL8/78) | Reference sequences with SNPs % |
---|---|---|---|---|
Group by combinations of sequencing platforms and DNA sources (SNP filtered with merged SNPs discovered by three sequencing platforms) | ||||
Roche 454(genomic) | 17,228 | 8.81 | 10,199 | 6.69 |
Solexa(genomic) | 17,434 | 8.91 | 14,130 | 9.27 |
Solexa(genomic)/Roche 454(genomic) | 960 | 0.49 | 863 | 0.57 |
SOLiD(cDNA) | 36,667 | 18.75 | 31,963 | 20.98 |
SOLiD(cDNA)/Roche 454(genomic) | 106 | 0.05 | 105 | 0.07 |
SOLiD(cDNA)/Solexa(genomic) | 879 | 0.45 | 860 | 0.56 |
SOLiD(cDNA)/Solexa(genomic)/Roche 454(genomic) | 21 | 0.01 | 21 | 0.01 |
SOLiD(genimc)/Solexa(genomic)/Roche 454(genomic) | 95 | 0.05 | 92 | 0.06 |
SOLiD(genomic) | 102,902 | 52.60 | 76,267 | 50.05 |
SOLiD(genomic)/Roche 454(genomic) | 424 | 0.22 | 413 | 0.27 |
SOLiD(genomic)/Solexa(genomic) | 3,567 | 1.82 | 3,280 | 2.15 |
SOLiD(genomic)/SOLiD(cDNA) | 14,968 | 7.65 | 13,812 | 9.06 |
SOLiD(genomic)/SOLiD(cDNA)/Roche 454(genomic) | 19 | 0.01 | 19 | 0.01 |
SOLiD(genomic)/SOLiD(cDNA)/Solexa(genomic) | 351 | 0.18 | 348 | 0.23 |
Total | 195,631 | 100.00 | 152,372 | 100.00 |
Group by single sequencing platform or DNA source (SNP filtered with merged SNPs discovered by three sequencing platforms) | ||||
SOLiD(genomic) (~10.7 X)(b) | 122,326 | 62.53 | 94,231 | 61.84 |
SOLiD(cDNA) (~21.5X) | 53,021 | 27.10 | 47,128 | 30.93 |
Solexa(genomic) (~2.1X) | 23,307 | 11.91 | 19,594 | 12.86 |
Roche 454(genomic) (~1.6X) | 18,853 | 9.64 | 11,712 | 7.69 |
Total(c) | 217,507 | 111.18 | 172,665 | 113.32 |
SNPs filtered by individual sequencing platforms | ||||
SOLiD(genomic) (~10.7 X)(b) | 55,657 | 72.67 | 50,639 | 76.50 |
SOLiD(cDNA) (~21.5X) | 17,935 | 23.42 | 16,726 | 25.27 |
Solexa(genomic) (~2.1X) | 7,729 | 10.09 | 7,323 | 11.06 |
Roche 454(genomic) (~1.6X) | 2,210 | 2.89 | 1,979 | 2.99 |
Total(d) | 83,531 | 109.07 | 76,667 | 115.83 |