Table 3 |
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|
Validation of SNPs detected by QualitySNP and autoSNP in nineteen UniGene data sets of human. |
|||||||||||||
|
QualitySNP(D < = 0.6) |
autoSNP |
their overlap |
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|
|
|||||||||||||
|
chromosome |
UniGene |
Size |
Time(m) |
candidate SNPsa |
confirmed |
unconfirmed |
Time(m) |
candidate SNPsb |
confirmed |
unconfirmed |
candidate SNPs |
confirmed |
unconfirmed |
|
|
|||||||||||||
|
6 |
Hs.300701 |
3640 |
2 |
18 |
5 (27.8%) |
13 |
150 |
6 |
0 (0%) |
6 |
3 |
0(0%) |
3 |
|
7 |
Hs.401316 |
1090 |
1 |
0 |
0 (0%) |
0 |
3 |
4 |
0 (0%) |
4 |
0 |
0(0%) |
0 |
|
14 |
Hs.533717 |
1601 |
1 |
12 |
3 (25%) |
9 |
26 |
166 |
1 (0.6%) |
165 |
0 |
0(0%) |
0 |
|
17 |
Hs.12956 |
622 |
1 |
10 |
2 (20%) |
8 |
1 |
15 |
1 (6.7%) |
14 |
9 |
1(11.11%) |
8 |
|
19 |
Hs.515126 |
654 |
1 |
1 |
0 (0%) |
1 |
2 |
44 |
0 (0%) |
44 |
1 |
0(0%) |
1 |
|
15 |
Hs.22543 |
847 |
1 |
10 |
1 (10%) |
9 |
1 |
4 |
1 (25%) |
3 |
1 |
1(100%) |
0 |
|
2 |
Hs.468478 |
183 |
1 |
0 |
0 (0%) |
0 |
1 |
0 |
0 (0%) |
0 |
0 |
0(0%) |
0 |
|
1 |
Hs.591503 |
200 |
1 |
6 |
2 (33.3%) |
4 |
1 |
5 |
0 (0%) |
5 |
3 |
0(0%) |
3 |
|
6 |
Hs.567284 |
194 |
1 |
7 |
0 (0%) |
7 |
1 |
8 |
0 (0%) |
8 |
7 |
0(0%) |
7 |
|
6 |
Hs.510172 |
282 |
1 |
1 |
0 (0%) |
1 |
1 |
0 |
0 (0%) |
0 |
0 |
0(0%) |
0 |
|
17 |
Hs.406754 |
6453 |
2 |
49 |
25 (51%) |
24 |
51 |
43 |
6 (14%)) |
37 |
14 |
5(35.71%) |
9 |
|
14 |
Hs.510635 |
27193 |
4 |
535 |
198 (37%) |
337 |
13 |
895 |
92 (10.3%) |
803 |
143 |
86(60.14%) |
57 |
|
7 |
Hs.61635 |
82 |
1 |
0 |
0 (0%) |
0 |
1 |
0 |
0 (0%) |
0 |
0 |
0(0%) |
0 |
|
2 |
Hs.631881 |
355 |
1 |
5 |
0 (0%) |
5 |
1 |
1 |
0 (0%) |
1 |
0 |
0(0%) |
0 |
|
8 |
Hs.104741 |
275 |
1 |
0 |
0 (0%) |
0 |
1 |
0 |
0 (0%) |
0 |
0 |
0(0%) |
0 |
|
2 |
Hs.534639 |
1910 |
1 |
11 |
1 (9.1%) |
10 |
6 |
9 |
0 (0%) |
9 |
6 |
0(0%) |
6 |
|
14 |
Hs.18069 |
1965 |
1 |
3 |
1 (33.3%) |
2 |
1 |
1 |
0 (0%) |
1 |
0 |
0(0%) |
0 |
|
17 |
Hs.514220 |
6800 |
2 |
8 |
2 (25%) |
6 |
267 |
13 |
0 (0%) |
13 |
2 |
0(0%) |
2 |
|
12 |
Hs.19192 |
397 |
1 |
1 |
0 (0%) |
1 |
2 |
0 |
0 (0%) |
0 |
0 |
0(0%) |
0 |
|
|
|||||||||||||
|
Total |
54743 |
677 |
240 (35.5%) |
437 |
1214 |
101 (8.3%) |
1113 |
189 |
93(49.21%) |
96 |
|||
|
|
|||||||||||||
|
a Candidate SNPs predicted by QualitySNP; b candidate SNPs (score > = 50) predicted by autoSNP. confirmed: Candidate SNPs are considered as confirmed if they are present in dbSNP. Time (m): the minutes were used to run a program on each UniGene. |
|||||||||||||
|
Tang et al. BMC Bioinformatics 2006 7:438 doi:10.1186/1471-2105-7-438 |
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