Table A1.5.
The percentage of SNP pairs for all pairs on the same chromosome for which both SNPs occur within a block, for different block sizes (kb) for Cortex, GATK, Samtools Mpileup and Pileup (Supplementary Table 6). Singletons may have clustered for Samtools Pileup, but not for Cortex, GATK or Samtools Mpileup. The mean distance was calculated the average distance between SNPs of the given type on the same chromosome. Non-rare SNPs were those found in three or more samples.
SNP Caller |
SNP type |
Block size (kb) |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
0.01 |
0.1 |
0.5 |
1 |
5 |
10 |
50 |
100 |
500 |
||
Cortex |
Non-rare |
0.0 |
0.3 |
0.9 |
1.1 |
1.7 |
3.4 |
9.6 |
17.0 |
61.5 |
Doubletons |
1.5 |
1.5 |
1.5 |
1.5 |
3.1 |
3.1 |
10.8 |
13.8 |
64.6 |
|
Singletons |
0.0 |
0.0 |
0.0 |
0.0 |
3.8 |
3.8 |
23.1 |
30.8 |
80.8 |
|
All |
0.0 |
0.3 |
0.9 |
1.1 |
1.7 |
3.3 |
9.6 |
17.0 |
61.5 |
|
GATK |
Non-rare |
0.0 |
0.1 |
0.2 |
0.3 |
1.1 |
2.1 |
9.3 |
17.8 |
64.4 |
Doubletons |
1.3 |
1.3 |
1.3 |
1.3 |
1.3 |
1.3 |
5.3 |
13.3 |
61.3 |
|
Singletons |
0.0 |
0.0 |
0.0 |
0.0 |
1.1 |
3.2 |
11.8 |
18.3 |
77.4 |
|
All |
0.0 |
0.1 |
0.2 |
0.3 |
1.1 |
2.1 |
9.3 |
17.8 |
64.4 |
|
Samtools Mpileup |
Non-rare |
0.0 |
0.1 |
0.3 |
0.4 |
1.2 |
2.2 |
9.5 |
17.9 |
64.4 |
Doubletons |
0.0 |
0.0 |
0.0 |
0.0 |
6.7 |
6.7 |
6.7 |
20.0 |
60.0 |
|
Singletons |
0.0 |
0.0 |
0.0 |
0.0 |
9.1 |
9.1 |
9.1 |
9.1 |
81.8 |
|
All |
0.0 |
0.1 |
0.3 |
0.4 |
1.2 |
2.2 |
9.5 |
17.9 |
64.4 |
|
Samtools Pileup |
Non-rare |
0.0 |
0.1 |
0.2 |
0.3 |
1.1 |
2.1 |
9.3 |
17.8 |
64.4 |
Doubletons |
2.6 |
3.3 |
3.3 |
3.3 |
5.3 |
6.6 |
11.8 |
21.1 |
63.2 |
|
Singletons |
0.8 |
4.4 |
5.2 |
5.2 |
5.7 |
6.3 |
13.4 |
24.9 |
71.6 |
|
All |
0.0 |
0.1 |
0.2 |
0.3 |
1.1 |
2.1 |
9.3 |
17.8 |
64.5 |
|