Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms

Table 2 Overview of SNP discovery and genotype calling using three different callers

	GATK_v.2.5-0			CLC_v.5.0.1			SAMtools_v.0.1.19
	Pop_SK	Pop_WA	Overall	Pop_SK	Pop_WA	Overall	Pop_SK	Pop_WA	Overall
No. of SNPs	34257	40248	57396	34788	55585	75364	14494	14903	24103
No. of private SNPs	17148	23139	40287	19779	40576	60355	9200	9609	18809
% singletons	7.68	10.83	12.18	11.53	27.47	25.59	14.63	21.66	22.19
Median site heterozygosity^a	0.267	0.250	/	0.236	0.200	/	0.266	0.231	/
Median coverage per individual	93×	70×	82×	66×	29×	48×	66×	19×	27×
	GATK-CLC _intersect			SAMtools- GATK _intersect			SAMtools-CLC _intersect
	Pop_SK	Pop_WA	Overall	Pop_SK	Pop_WA	Overall	Pop_SK	Pop_WA	Overall
No. of SNPs	21475	24936	37085	11325	12350	18933	9861	11310	17163
No. of private SNPs	12149	15610	27759	6583	7608	14191	5853	7302	13155
% singletons	9.91	17.98	12.82	9.99	20.53	19.37	10.54	23.08	21.60
Median site heterozygosity^a	0.250	0.222	/	0.286	0.231	/	0.266	0.222	/
Median coverage per individual^b	107× (65)	81× (27)	96× (37)	55× (98)	18× (98)	20× (99)	69× (76)	19× (35)	26× (46)

We required all SNPs to have a genotype call passing all stringent quality filters in a minimum of eight individuals per population (population-based filtering). The intersect datasets contain exclusively concordant genotype calls between the designated SNP callers. Pop_SK: South Kinabatangan population, Pop_WA: West Alas population.
^aBased on the sites being polymorphic within the population.
^bCoverage values of intersect datasets are taken from the first named SNP caller. The coverage values of the second named caller are given in brackets.

ISSN: 1471-2164