Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries

Table 2 RRL construction simulated by an in silico Alu I digest of the WASHUC2 build of the reference chicken genome

Line	Size-range	Number of fragments	Genome fraction	Sequenced (32 bp reads)	RRL coverage calculated
Layers	150-200	583826	101 Mb (8%)	18.7 Mb (1.5%)	37-40X
Broilers	125-200	947538	151 Mb (12%)	30.3 Mb (2.4%)	22-26X

Fragments were collected in corresponding size ranges as used in the in vitro RRL preparation. The total number of collected fragments and number of bases captured are indicators of what genome fraction was sampled. Based on trimmed reads, the fraction of the genome actually sequenced was calculated. The number of raw read pairs obtained (see Table 1) divided by the number of fragments is an indicator of the RRL coverage.

ISSN: 1471-2164