Analysis of five deep-sequenced trio-genomes of the Peninsular Malaysia Orang Asli and North Borneo populations

BMC Genomics

Table 1 Summary of sequence alignment and variants calling

	Bateq			Mendriq			Semai				Dusun			Murut
	BTQ016	BTQ038	BTQ055	MDQ010	MDQ025	MDQ045	SMI018	SMI034	SMI041	NB07	NB08	NB09	NB10	NB11	NB12
Sequencing depth	37.71	36.34	37.55	35.72	28.32	35.38	36.03	36.26	36.55	35.79	37.44	37.56	36.96	37.73	36.52
Bases covered percentage
Phred score ≥ 5	98.34	98.3	97.78	97.68	97.44	98.12	98.29	97.79	98.32	98.3	97.79	98.35	98.35	97.8	98.31
Phred score ≥ 10	97.83	97.73	97.35	97.11	96.23	97.29	97.75	97.36	97.78	97.71	97.37	97.82	97.8	97.38	97.77
Ti/Tv ratio	2.105	2.114	2.106	2.105	2.096	2.105	2.107	2.107	2.115	2.1	2.098	2.101	2.105	2.096	2.103
Novel variant proportion (%)
SNPs	1.19	1.16	1.21	0.87	0.68	1.03	0.69	0.70	0.69	0.32	0.34	0.34	0.33	0.33	0.33
Indels	1.49	1.48	1.47	1.34	1.23	1.41	1.28	1.25	1.29	1.11	1.08	1.12	1.12	1.06	1.11
Heterozygous variant proportion (%)
SNPs	52.56	51.63	53.53	56.63	54.94	54.12	53.44	54.68	52.03	52.60	53.70	52.88	52.30	54.78	52.6
indels	59.96	59.53	60.91	66.85	65.24	64.79	60.44	62.04	59.67	60.50	61.42	61.75	60.18	62.12	60.14
Number of variants in different types
Synonymous SNPs	11,433	11,455	11,530	11,685	11,414	11,563	11,625	11,512	11,482	11,302	11,290	11,212	11,522	11,427	11,433
Non-symonymous SNPs	10,902	10,827	10,876	11,109	10,865	10,810	11,051	10,947	10,783	10,753	10,688	10,865	10,825	10,786	10,729
Stop-loss	31	27	28	26	21	29	24	24	23	26	31	34	30	29	27
Stop-gain	88	86	99	104	100	97	101	92	103	111	107	111	93	104	99
Small frameshift indels	345	332	346	317	291	312	337	329	332	311	310	323	327	352	344

ISSN: 1471-2164