Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome

Table 2 Annotation of known repeats in core elements with large CNV and without CNV

					Expected copy number^c
Core element	Type	Length (bp)	Known repeats and RefSeq genes ^a	Ratio^b	B6	BLG2	MSM	Probe (N)	Total length in
									B6 (bp)
Core element 042	Constant	3000	LINE, Vmn2r , LTR	0.610	9	10	9	252	27000
Core element 108	Constant	3000	Cbx3 , LTR, SINE	0.250	3	3	3	154	9000
Core element 127	Constant	2700	Vmn2r , LINE	0.158	12	13	13	196	32400
Core element 244	Constant	3247	LINE, Vmn2r , SINE	0.563	8	8	8	68	25976
Core element 352	Constant	3900	LINE,LTR, Simple, SINE	0.911	8	8	8	264	31200
Core element 454	Constant	3372	Vmn2r, LINE	0.123	11	10	11	348	37092
Core element 462	Constant	2700	LINE, SINE,	0.910	6	7	6	40	16200
Core element 484	Constant	3000	LINE, Simple, SINE	0.839	4	4	4	54	12000
AVERAGE (Constant)		3115		0.545	8	8	8	172	23859
Core element 103.1	CNV	1802	LTR, SINE	0.959	14	20	19	127	25228
Core element 103.2	CNV	1686	Zfp , LINE, LTR	0.225	8	15	12	129	13488
Core element 146	CNV	2877	LINE, SINE	0.979	19	33	26	103	54663
Core element 154	CNV	2691	LTR, SINE	0.749	24	30	28	236	64584
Core element 177.1	CNV	3900	Simple, Zfp	0.110	23	28	27	112	89700
Core element 182	CNV	2629	LINE, LTR, MurSatRep1	0.622	20	27	25	305	52580
Core element 364	CNV	1468	SINE, LTR	0.343	13	16	18	190	19084
Core element 447	CNV	2248	LTR, SINE, Simple/Sat	0.768	24	35	30	108	53952
Core element 510	CNV	2735	LINE, Simple/Sat	0.094	13	19	16	348	35555
Core element 541	CNV	3195	Simple/Sat, Zfp	0.076	14	21	20	413	44730
AVERAGE (CNV)		2523		0.492	17	24	22	207	45356

^a Detailed information on the known repeats and RefSeq genes that were detected in each core element is provided in Additional file 5. LTR retrotransposons are underlined. Core elements with large CNV were selected by two criteria: 1) a P value lower than the significance value; 2) the 10 core elements that showed the greatest variation among strains. ^b Proportion of each core element that comprised the known repeat. The proportion was calculated by dividing the total length of the known repeat in the core element by the total length of the core element. ^c Expected copy numbers in B6 were calculated from the number of homologous sequences in each of the 60 groups (Additional file 5). Expected copy numbers in BLG2 and MSM were calculated from the average of the aCGH values and the copy number in B6 (Additional file 7).

ISSN: 1471-2164