Skip to main content

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.