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

Table 4 Annotation and SNP discovery using Roche 454 reads of genomic DNA of Ae. tauschi i AL8/78 as reference sequences

Category	No. of reads^(a)	Length in Mb (%)	Predicted single-copy reads	Length in Mb	No. of contigs and singletons	Length in Mb	No. of SNPs	Nucleotides/SNP	No. of annotated genes
Genes
Characterized	948,379	380.0 (8.0%)	734,848	298.8	378,152	153.4	153,787	997	32,307
Uncharacterized	285,529	113.7(2.3%)	109,158	44.0	45,570	18.1	41,844	432
Sub total	1,233,908	493.7 (10.3%)	844,066	342.8	423,722	171.5	195,631	876	32,307
Repetitive sequences
Characterized repeats	7,121,948	2,818.1 (59.0%)
Repeat junctions^(b)	347,811	156.9(3.3%)	200,564	89.3	200,564	89.3	145,907	612
Sub total	7,121,948	2,818.1 (59.0%)
Uncharacterized sequences	3,929,444	1,460.7 (30.7%)	2,398,762	891.2	1,236,912	271.5	155,580	1745
Total	12,285,300	4,772. 5 (100%)	3,443,392	1,323	1,861,198	532.3	497,118	1070	32,307

(a) Number of reads after removing chloroplast and mitochondrial reads and artificial replicates using the cd-hit-454 program [27] at 98% alignment identity and 90% of sequence coverage. (b) Repeat junctions are identified from characterized repeat sequences using the repeat junction annotation pipeline program (Table S1 in Additional file 1).

ISSN: 1471-2164