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 heterozygositya |
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 heterozygositya |
0.250 |
0.222 |
/ |
0.286 |
0.231 |
/ |
0.266 |
0.222 |
/ |
| Median coverage per individualb | 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.