Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

BMC Genomics

Table 1 Summary statistics for sequencing and CNVs of 12 individuals

Chicken abbreviation^a	Numbers of mapped reads	Depth	Coverage (%)	Autosome reads per 5 kb window^b	Autosome reads STDEV	Duplications	Deletions	Sequence covered (Mb)
BY	102,002,937	9.7	97.0	489.29	110.73	1,319	602	34.1
CS	85,383,494	8.2	96.9	409.93	101.42	1,132	663	26.8
DX	129,847,015	12.4	97.4	623.50	130.46	552	820	8.2
LX	105,152,881	10.0	97.3	503.82	112.74	898	821	11.7
RIR	102,464,756	9.8	97.3	490.96	108.21	578	669	8.3
RJF	105,517,587	10.1	97.2	504.23	113.52	702	620	9.8
SG	85,987,827	8.2	96.6	412.27	87.66	470	553	7.2
SK	95,322,371	9.1	97.1	457.21	100.61	773	657	12.3
TB	107,535,104	10.3	97.3	515.68	108.07	607	679	8.5
WC	119,116,969	11.4	97.4	572.35	121.39	710	768	9.8
WL	118,689,980	11.3	97.5	567.18	118.63	203	441	3.3
WR	130,307,416	12.4	97.6	625.01	132.32	224	477	3.3

^aBY Beijing You, CS Cornish, DX Dongxiang, LX Luxi Game, RIR Red Island Rhode, RJF Red Jungle Fowl, SG Shouguang, SK Silkie, TB Tibetan, WC Wenchang, WL White Leghorn, WR White Plymouth Rock.
^bThe number of reads per 5 kb windows after GC correction.

ISSN: 1471-2164