Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries

BMC Genomics

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 depth^a	Average mapping coverage (%)^b
Genotype	Read length (bp)	Number of PET reads	Length (Mbp)	Genome equivalent (X)	Number of PET reads (%)	Length (Mbp)	Number of PET reads	Length (Mbp)	Average mapped read depth^a	Average mapping coverage (%)^b
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 ( $\bar{X}$ )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).

ISSN: 1471-2164