/EXTERNAL Roadmap/variants/K006500_K006501_2_lane_gembs
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SAMPLE K006500_K006501_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156502749 |
1073283676 |
92.80 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156502749 |
100% |
1148783064 |
99.33 % |
7719685 |
0.67 % |
| |
|
|
|
|
|
|
| Passed |
1073457114 |
92.82 % |
1069929482 |
93.14 % |
3527632 |
0.33 % |
| Filtered |
83045635 |
7.18 % |
78853582 |
6.86 % |
4192053 |
0.39 % |
| |
|
|
|
|
|
|
| mq40 |
43514198 |
52.40 % |
42911024 |
54.42 % |
603174 |
14.39 % |
| q20,mq40 |
18242798 |
21.97 % |
18011914 |
22.84 % |
230884 |
5.51 % |
| q20 |
14156386 |
17.05 % |
13891912 |
17.62 % |
264474 |
6.31 % |
| q20,qd2 |
2710259 |
3.26 % |
675433 |
0.86 % |
2034826 |
48.54 % |
| q20,qd2,mq40 |
2386466 |
2.87 % |
1762797 |
2.24 % |
623669 |
14.88 % |
| qd2 |
1663497 |
2.00 % |
1381619 |
1.75 % |
281878 |
6.72 % |
| qd2,mq40 |
279913 |
0.34 % |
218883 |
0.28 % |
61030 |
1.46 % |
| fs60 |
35606 |
0.04 % |
0 |
0.00 % |
35606 |
0.85 % |
| q20,qd2,fs60 |
34241 |
0.04 % |
0 |
0.00 % |
34241 |
0.82 % |
| fs60,mq40 |
9276 |
0.01 % |
0 |
0.00 % |
9276 |
0.22 % |
| q20,fs60 |
9158 |
0.01 % |
0 |
0.00 % |
9158 |
0.22 % |
| qd2,fs60 |
2490 |
0.00 % |
0 |
0.00 % |
2490 |
0.06 % |
| q20,qd2,fs60,mq40 |
777 |
0.00 % |
0 |
0.00 % |
777 |
0.02 % |
| qd2,fs60,mq40 |
434 |
0.00 % |
0 |
0.00 % |
434 |
0.01 % |
| q20,fs60,mq40 |
136 |
0.00 % |
0 |
0.00 % |
136 |
0.00 % |
Coverage and Quality
| Coverage Variants |
Quality Variants |
 |
 |
Filtering Criteria Distribution
| Phred scale strand bias estimated using Fisher's Exact Test. |
 |
| Allele-specific call confidence normalized by depth of sample reads supporting the allele. Variants. |
Allele-specific call confidence normalized by depth of sample reads supporting the allele. Non-Variants. |
 |
 |
| Root Mean Square of the mapping quality of reads. Variants. |
Root Mean Square of the mapping quality of reads. Non-Variants. |
 |
 |
Mutations
| Type |
Mutation |
Status |
# |
% |
| Transition |
A>G |
All |
2288867 |
25.05 % |
| Transition |
G>A |
All |
1004626 |
10.99 % |
| Transition |
T>C |
All |
2288265 |
25.04 % |
| Transition |
C>T |
All |
1020796 |
11.17 % |
| Transversion |
A>C |
All |
255533 |
2.80 % |
| Transversion |
C>A |
All |
377663 |
4.13 % |
| Transversion |
T>G |
All |
257196 |
2.81 % |
| Transversion |
G>T |
All |
385923 |
4.22 % |
| Transversion |
A>T |
All |
393453 |
4.31 % |
| Transversion |
T>A |
All |
378046 |
4.14 % |
| Transversion |
C>G |
All |
241760 |
2.65 % |
| Transversion |
G>C |
All |
245003 |
2.68 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
820898 |
18.28 % |
| Transition |
G>A |
Passed |
706677 |
15.74 % |
| Transition |
T>C |
Passed |
833353 |
18.56 % |
| Transition |
C>T |
Passed |
715995 |
15.95 % |
| Transversion |
A>C |
Passed |
183410 |
4.08 % |
| Transversion |
C>A |
Passed |
179409 |
4.00 % |
| Transversion |
T>G |
Passed |
183285 |
4.08 % |
| Transversion |
G>T |
Passed |
180145 |
4.01 % |
| Transversion |
A>T |
Passed |
162898 |
3.63 % |
| Transversion |
T>A |
Passed |
161824 |
3.60 % |
| Transversion |
C>G |
Passed |
180369 |
4.02 % |
| Transversion |
G>C |
Passed |
181908 |
4.05 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPAll |
0 |
0.00 % |
| Transition |
G>A |
dbSNPAll |
0 |
0.00 % |
| Transition |
T>C |
dbSNPAll |
0 |
0.00 % |
| Transition |
C>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPAll |
0 |
0.00 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPPassed |
0 |
0.00 % |
| Transition |
G>A |
dbSNPPassed |
0 |
0.00 % |
| Transition |
T>C |
dbSNPPassed |
0 |
0.00 % |
| Transition |
C>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPPassed |
0 |
0.00 % |
| |
|
|
|
|
Ti/Tv Ratio
| Status |
Ratio |
Transitions |
Transversions |
| All |
2.60 |
6602554 |
2534577 |
| Passed |
2.18 |
3076923 |
1413248 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |