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Table 5 Comparison of single-copy read predictions by different sequencing platforms mapped to characterized gene contigs (including singletons) of Ae. tauschi i accession AL8/78 sequenced with Roche 454

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 and DNA source

Roche 454 contigs mapped

Contigs shared with SOLiD(a)

Cut-off value for single-copy prediction

Single- copy Roche 454 contigs (% of mapped contigs)

Single-copy contigs shared(a)

Contingency χ2test P value

SOLiD (~10.7X)(b)

378,185

 

53

347,199 (91.8%)

  

Solexa (~2.1X)

305,495

299,673

8

281,513 (92.2%)

260,261 (86.8%)

0.0001

Roche 454 (~1.6X)

104,030

101,800

8

97,399 (93.6%)

78,963 (77.6%)

0.0001

  1. (a) Number of Roche 454 contigs to which reads generated with an indicated platform and SOLiD were mapped. (b) The coverage estimate is the average depth of sequences mapped to Roche 454 contigs.
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BMC Genomics

ISSN: 1471-2164

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