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

Table 4 Validation structural polymorphisms

Structural variants (SV) 13-18 were chosen before application of the empirical rule (span-size deviation) × n >500, whereas 50-59 were chosen after. Span size is the distance (in base pairs) on the reference sequence spanned by discordantly mapping read pairs. The number of observed discordantly mapping read pairs that support the presence of this structural variant is given by n. CMP is flagged in case there were also concordantly mapping read pairs observed in that particular genomic region. Discordantly mapping read pairs spanning an assembly problem in the reference genome are flagged in the RE column. The alternative mapping quality of a predicted SV is the average mapping quality calculated over discordantly mapping read pairs within a cluster. Deletion breakpoints are in the notation chr_start-stop, whereas insertion breakpoints are given in the notation chr_position. Not acquired (NA) breakpoints were due to false positive SV predictions whereas breakpoints for SV27 were not acquired for technical reasons and not accurately acquired in SV50 due to low sequence complexity. W = white egg layer; B = brown egg layer; 1 = broiler 1; 2 = broiler 2.
*Due to the low sequence complexity, the exact location of insertion could not be revealed

ISSN: 1471-2164