|
Sampling
|
0.005
|
0.01
|
0.02
|
0.05
|
0.10
|
0.20
|
0.30
|
0.40
|
|
Expected mean coverage
|
0.10
|
0.19
|
0.39
|
0.97
|
1.94
|
3.88
|
5.82
|
7.76
|
|
Achieved mean coverage
|
0.09
|
0.19
|
0.38
|
0.94
|
1.88
|
3.75
|
5.63
|
7.51
|
|
Cov % of genome ≥1 read
|
8.70 %
|
16.47 %
|
29.71 %
|
56.28 %
|
76.85 %
|
88.41 %
|
90.69 %
|
91.28 %
|
|
Cov % of genome by ANGSD
|
8.64 %
|
16.37 %
|
29.55 %
|
56.06 %
|
76.68 %
|
88.35 %
|
90.67 %
|
91.27 %
|
|
% of correctly called bases
|
99.72 %
|
99.73 %
|
99.74 %
|
99.77 %
|
99.82 %
|
99.89 %
|
99.92 %
|
99.93 %
|
- The first row refers to the percentage of reads that were randomly sampled from the original data set (LBK/Stuttgart) from Lazaridis et al. [19] (coverage ≈19×) using SAMtools. The expected mean coverage was derived by multiplication of the original coverage with the sampling value. The achieved mean coverage was calculated using QualiMap after mapping. Cov % of genome ≥1 read is the percentage of the genome that was covered by at least one read. This was also calculated using QualiMap. Cov % of genome by ANGSD is the percentage of the genome that was reconstructed from the genotypes as derived with ANGSD. % of correctly called bases is the percentage of bases that ANGSD called correctly not regarding the base “N”
