An initial map of chromosomal segmental copy number variations in the chicken

BMC Genomics

Table 1 High confidence CNVs in chickens

Locus ID	Chromosome	Start position*	Size (bp)	Gene	Status ^#			Number of observations
					Broiler	Leghorn	RIR^†
1	1	4015022	47654	LOC419112	loss	loss	loss	6
2	1	44980061	80399	Non-coding	loss	loss		7
3	1	48005486	34931	Non-coding	gain			3
4	1	59885173	32693	CHRM2		loss		2
5	1	165880299	112347	ZFR, IL-3	gain	gain		4
6	2	40647961	39933	Spliced ESTs		gain	loss	2
7	2	95665092	10297	Non-coding	gain	gain		4
8	2	97295434	44839	Non-coding	gain	gain		5
9	2	134727846	102330	MGC24975(SZD6)	gain	gain		3
10	2	154562776	299829	SCRIB	loss	gain		2
11	3	113612615	40053	MRPL19,	loss		loss	2
12	4	62172811	12364	Non-coding	loss		loss	2
13	4	88897639	175343	RHACD8	gain	loss	loss	5
14	4	89602897	42219	Non-coding		loss		3
15	5	22120222	92556	Non-coding		loss		3
16	6	12150334	84982	Non-coding		loss	loss	3
17	10	125113	32851	olfactory receptor 6k2	gain	gain		2
18	11	2670295	14897	Non-coding	gain			3
19	12	15208	77317	Non-coding	loss			2
20	13	2722503	60308	EST	loss		loss	3
21	16	200114	12820	Zinc finger protein	loss	loss		2
22	16	270019	162832	HLA class I antigen	loss	loss		2
23	17	567532	57890	PRF1	gain			2
24	Z	9965426	192201	PRLR	loss	loss		2
25	Z	71975037	142814	CDKN2A, MTAP	loss	loss	loss	3
26	Z	73495364	29964	Non-coding	gain	gain		2

Note: *, the start position of the CNV was based on 2006 chicken genome assembly. #, gain or loss was assigned based on common reference DNA from one broiler bird (#6281). †, Rhode Island Red.

ISSN: 1471-2164