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Table 6 SNP discovery in Ae. tauschi i genes using different sequencing platforms and DNA sources

From: Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

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
  1. (a) Three different sequencing platforms (Roche 454, Solexa and SOLiD) and two DNA sources (Genomic DNA and cDNA) were used in SNP discovery. SNPs were counted by combinations of sequencing platforms and DNA sources or individual sequencing platform/DNA sources. (b) Genome coverage in parentheses was estimated from the length of mapped gene reference sequences and mapped read depths (See Figure 2). (c) If SNPs were filtered by merged SNPs from three sequencing platforms, the total number of SNPs and reference sequences with at least one SNP are 195,631 and 152,372, respectively. Because the same SNPs may be discovered by both cDNA and genomic reads, or by more than one sequencing platforms, the sum of SNPs in grouping by single sequencing platform or DNA source exceeds the actual number of SNPs. The difference will be the number shared by two DNA sources or multiple sequencing platforms. The same is true for number of reference sequences and percentage values in the table. (d) If SNPs were filtered by individual sequencing platforms (run the entire SNP discovery pipeline by individual sequencing platforms), the total number of unique SNPs discovered and reference sequences with at least one SNP were 76,588 and 66,190, respectively. For the same reason as (c), the sum of SNPs discovered by single sequencing platform or DNA source exceeds the actual SNPs.
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