The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements

Marques-Bonet, Tomàs; Cheng, Ze; She, Xinwei; Eichler, Evan E; Navarro, Arcadi

doi:10.1186/1471-2164-9-384

Table 3 Average of divergences and lengths among paralogous copies of SDs relative to genomic factors and rearrangements between human and chimpanzees.

From: The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements

Sex Chromosomes				ID
	SDs in Autosomes	SDs in HSAX	P-value	> 98%
N	889	103
K	0.0107	0.0076	< 0.001
Size	41,439.50	52,887.93	0.115
	SDs in Autosomes	SDs in HSAX	P-value	< 92%
N	3273	261
K	0.0958	0.0962	0.364
Size	4,689.73	4,458.48	0.578
	SDs in Autosomes	SDs in HSAY	P value	> 98%
N	889	32
K	0.0107	0.0052	< 0.001
Size	41,439.50	########	< 0.001
	SDs in Autosomes	SDs in HSAY	P value	< 92%
N	3273	132
K	0.0958	0.0976	0.001
Size	4,689.73	12,290.17	< 0.001
Telomeres (10 Mb)				ID
	SDs not in telomeres	SDs in Telomeres	P-value	> 98%
N	719	170
K	0.0105	0.0115	0.052
Size	44,040.90	30,437.11	0.01
	SDs not in telomeres	SDs in Telomeres	P-value	< 92%
N	2831	442
K	0.0958	0.0958	0.874
Size	4,746.56	4,325.72	0.224
Centromere (5 Mb)				ID
	SDs not in Centromeres	SDs in Centromeres	P-value	> 98%
N	572	147
K	0.0106	0.01	0.316
Size	36,111.33	74,896.07	< 0.001
	SDs not in Centromeres	SDs in Centromeres	P-value	< 92%
N	2096	735
K	0.0959	0.0953	0.029
Size	3,908.13	7,137.51	< 0.001
HSA19				ID
	SDs in other autosomes	SDs in HSA19	P-value	> 98%
N	561	11
K	0.0105	0.0126	0.32
Size	36,600.01	11,188.90	0.139
	SDs in other autosomes	SDs in HSA19	P-value	< 92%
N	2029	67
K	0.0959	0.0958	0.906
Size	3,875.29	4,902.67	0.141
Rearranged Chromosomes				ID
	SDs in Colinear chr	SDs in Rearranged Chr	P-value	> 98%
N	208	353
K	0.0114	0.01	0.009
Size	25,385.48	43,208.01	< 0.001
	SDs in Colinear chr	SDs in Rearranged Chr	P-value	< 92%
N	890	1139
K	0.0959	0.096	0.902
Size	3,791.72	3,940.59	0.534
Inside rearranged regions versus Outside rearranged regions, without HSA2				ID
	SDs Outside rearranged regions	SDs Inside rearranged regions	P-value	> 98%
N	216	87
K	0.0104	0.0096	0.347
Size	40,400.12	55,156.56	0.058
	SDs Outside rearranged regions	SDs Inside rearranged regions	P-value	< 92%
N	715	267
K	0.096	0.0957	0.586
Size	3,879.46	4,868.64	0.016
Inversions detected in (Newman et al 2005) vs rest of chromosomes				ID
	SDs Outside Inversion	SDs Inside Inversion	P-value	> 98%
N	541	20
K	0.0104	0.0131	0.063
Size	35,170.62	75,264.90	0.003
	SDs Outside Inversion	SDs Inside Inversion	P-value	< 92%
N	1977	52
K	0.0959	0.0986	0.004
Size	3,853.94	4,686.98	0.281
Breakpoints versus inverted chromosomes (excluding HSA2)				ID
	SDs rest of Chr	SDs in BKP	P-value	> 98%
N	286	17
K	0.0103	0.008	0.135
Size	44,189.30	52,171.11	0.611
	SDs rest of Chr	SDs in BKP	P-value	< 92%
N	953	29
K	0.096	0.0941	0.15
Size	4,159.23	3,792.82	0.748

Divergence (K) is calculated as the number of substitution per site between the two duplication alignments. Length (Size) corresponds to the aligned basepairs. P-values are calculated by means of permutation test (see Material and Methods).

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ISSN: 1471-2164

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