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 4 Average of inter-specific divergences in human SDs and chimpanzee 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

HUMAN SD	X-Chromosome		Y-Chromosome		Telomeres vs. rest of genome		Centromeres vs. rest of genome		Chromosome 19
	vs. Autosomes		vs. Autosomes
	SDs in autosomes	SDs in the HSAX.	SDs in autosomes	SDs in the HSAY.	SDs outside Telomeres	SDs within Telomeres	SDs outside Centromeres	SDs within Centromeres	SDs outside HSA19	SDs within HSA19
N	1303	109	1303	51	1052	251	742	310	714	28
Divergence	0.0238	0.0161	0.0238	0.0259	0.0233	0.026	0.0228	0.0247	0.0225	0.0285
P-value		< 0.001		0.087		< 0.001		< 0.001		0.001
CHIMP SD	X-Chromosome		Y-Chromosome		Telomeres vs. rest of genome		Centromeres vs. rest of genome		Chromosome 19
	vs. Autosomes		vs. Autosomes
	SDs in autosomes	SDs in the HSAX.	SDs in autosomes	SDs in the HSAY.	SDs outside Telomeres	SDs within Telomeres	SDs outside Centromeres	SDs within Centromeres	SDs outside HSA19	SDs within HSA19
N	1415	110	1415	87	1224	191	789	435	779	10
Divergence	0.0222	0.0156	0.0222	0.0223	0.0217	0.0252	0.021	0.0231	0.0207	0.038
P-value		< 0.001		0.891		< 0.001		< 0.001		< 0.001
HUMAN SD	Rearranged vs.			SDs within vs.
	Colinear chromosomes			outside rearranged regions (excluding HSA2)
	SDs in colinear chr.	SDs in Rearranged chr.	P-value	SDs Outside inversions	SDs inside inversions	P-value
N	267	447		280	112
Divergence	0.0236	0.0219	0.01	0.0218	0.0219	0.934
CHIMP SD	Rearranged vs.			SDs within vs.
	Colinear chromosomes			outside rearranged regions (excluding HSA2)
	SDs in colinear chr.	SDs in Rearranged chr.	P-value	SDs Outside inversions	SDs inside inversions	P-value
N	256	523		312	160
Divergence	0.0216	0.0203	0.025	0.0202	0.0199	0.693
HUMAN SD	Breakpoints vs.
	inverted chromosomes
	(excludingHSA2)
	SDs in Rearranged chr.	SDs in BKPs	P-value
N	370	22
Divergence	0.0217	0.0242	0.136
CHIMP SD	Breakpoints vs.
	inverted chromosomes
	(excludingHSA2)
	SDs in Rearranged chr.	SDs in BKPs	P-value
N	441	31
Divergence	0.0201	0.0194	0.552
HUMAN SD	SDs within vs. outside rearranged regions
	(excluding breakpoints and HSA2)
	SDs Outside inversions	SDs inside inversions	P-value
N	264	106
Divergence	0.0216	0.022	0.619
CHIMP SD	SDs within vs. outside rearranged regions
	(excluding breakpoints and HSA2)
	SDs Outside inversions	SDs inside inversions	P-value
N	291	150
Divergence	0.0202	0.0199	0.583
HUMAN SD	inversions (Newman et al. 2005) versus rest chromosomes
	SDs Outside inversions	SDs inside inversions	P-value
N	670	44
Divergence	0.0227	0.0196	0.015
CHIMP SD	inversions (Newman et al. 2005) chromosomes
	SDs Outside inversions	SDs inside inversions	P-value
N	713	66
Divergence	0.021	0.0183	0.004

Divergence is calculated as the number of substitution per site between the two duplication alignments.

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com

BMC Genomics

Contact us