|
Softwarea
|
Grade or score thresholdb
|
Found SNPs (%)
|
Missed SNPs (%)
|
|---|
|
DiSNPindel
|
1
|
60 (90.9 %)
|
6 (9.1 %)
|
| |
2
|
61 (92.4 %)
|
5 (7.6 %)
|
| |
3
|
61 (92.4 %)
|
5 (7.6 %)
|
| |
4
|
63 (95.4 %)
|
3 (4.6 %)
|
| |
5
|
63 (95.4 %)
|
3 (4.6 %)
|
| |
6
|
63 (95.4 %)
|
3 (4.6 %)
|
|
novoSNP
|
18
|
0 (0.0 %)
|
66 (100.0 %)
|
| |
13
|
11 (16.7 %)
|
55 (83.3 %)
|
| |
9
|
16 (24.4 %)
|
50 (75.6 %)
|
| |
6
|
19 (28.8 %)
|
47 (71.2 %)
|
| |
3
|
25 (37.9 %)
|
41 (62.1 %)
|
| |
1
|
25 (37.9 %)
|
41 (62.1 %)
|
|
Mutation surveyor
|
Medium sensitivity
|
20 (30.3 %)
|
46 (69.7 %)
|
| |
High sensitivity
|
20 (30.3 %)
|
46 (69.7 %)
|
- The numbers of found and missed SNPs were experimentally verified with 66 CAPS-associated intra-individual SNPs originating from 62 single traces [22]
-
aPolyPhred did not detect any SNPs at ranks 1–6 and was thus excluded from the comparison
-
bGrade 2, score 13 and medium sensitivity could be a high threshold for reliable SNP detection in DiSNPindel, novoSNP and Mutation Surveyor, respectively, where Grade 4, score 6 and high sensitivity could be a low threshold
