Table 1

Summary of sequencing and read mapping of the Illumina GAIIx reads of the reduced representation libraries of eight flax genotypes
Genotype Read length (bp) Total Mapped Unmapped Average mapped read deptha Average mapping coverage (%)b
Number of PET reads Length (Mbp) Genome equivalent (X) Number of PET reads (%) Length (Mbp) Number of PET reads Length (Mbp)
CDC Bethune 50 34,290,788 1,715 5 31,817,354 (93) 1,591 2,473,429 (7) 124 11.20 8.83
Macbeth 50 32,815,888 1,641 4 30,297,145 (92) 1,515 2,518,739 (8) 126 7.86 13.97
SP2047 50 35,570,612 1,779 5 32,667,382 (92) 1,633 2,903,225 (8) 145 11.41 9.29
UGG5-5 50 32,046,570 1,602 4 29,139,577 (91) 1,457 2,906,989 (9) 145 10.24 8.62
Double Low 75 56,669,792 4,250 12 47,272,267 (83) 3,545 9,397,514 (17) 705 9.28 26.65
Crepitam Tabor 75 57,974,144 4,348 12 46,740,722 (81) 3,506 11,233,410 (19) 843 7.95 37.04
G-1186/94 100 57,867,644 5,787 16 45,245,067 (78) 4,525 12,622,561 (22) 1,262 9.61 26.77
Atlas 100 56,900,660 5,690 15 45,599,045 (80) 4,560 11,301,600 (20) 1,130 9.66 31.56
Total 364,136,098 26,812 73 308,778,559 22,332 55,357,467 4,480

Read mapping was performed against the whole genome shotgun sequence assembly (LinUsi_v1.1) of CDC Bethune using BWA.

a Average mapped read depth (<a onClick="popup('http://www.biomedcentral.com/1471-2164/13/684/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/13/684/mathml/M1">View MathML</a>)was based on a fitted extreme value distribution of mapped read depth in a bin width of 1 Kbp sequence.

b The average mapping coverage percentage was estimated based on the CDC Bethune reference genome sequence length of 302 Mbp (size of scaffolds without gaps).

Kumar et al.

Kumar et al. BMC Genomics 2012 13:684   doi:10.1186/1471-2164-13-684

Open Data