/EXTERNAL DEEP/variants/K006057_K006058_K006059_K006060_K006061_K006062_6_lane_gembs
BACK
SAMPLE K006057_K006058_K006059_K006060_K006061_K006062_6_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1172693293 |
739632093 |
63.07 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1172693293 |
100% |
1136971450 |
96.95 % |
35721843 |
3.05 % |
| |
|
|
|
|
|
|
| Passed |
745972124 |
63.61 % |
735877029 |
64.72 % |
10095095 |
1.35 % |
| Filtered |
426721169 |
36.39 % |
401094421 |
35.28 % |
25626748 |
3.44 % |
| |
|
|
|
|
|
|
| q20 |
379386706 |
88.91 % |
371204598 |
92.55 % |
8182108 |
31.93 % |
| q20,qd2 |
27118508 |
6.36 % |
10607876 |
2.64 % |
16510632 |
64.43 % |
| q20,mq40 |
10783777 |
2.53 % |
10605730 |
2.64 % |
178047 |
0.69 % |
| qd2 |
4902329 |
1.15 % |
4597396 |
1.15 % |
304933 |
1.19 % |
| q20,qd2,mq40 |
3023887 |
0.71 % |
2854210 |
0.71 % |
169677 |
0.66 % |
| mq40 |
1434597 |
0.34 % |
1169408 |
0.29 % |
265189 |
1.03 % |
| qd2,mq40 |
66646 |
0.02 % |
55203 |
0.01 % |
11443 |
0.04 % |
| qd2,fs60,mq40 |
1480 |
0.00 % |
0 |
0.00 % |
1480 |
0.01 % |
| qd2,fs60 |
1048 |
0.00 % |
0 |
0.00 % |
1048 |
0.00 % |
| fs60 |
720 |
0.00 % |
0 |
0.00 % |
720 |
0.00 % |
| q20,qd2,fs60 |
654 |
0.00 % |
0 |
0.00 % |
654 |
0.00 % |
| fs60,mq40 |
422 |
0.00 % |
0 |
0.00 % |
422 |
0.00 % |
| q20,qd2,fs60,mq40 |
394 |
0.00 % |
0 |
0.00 % |
394 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
12812204 |
33.90 % |
| Transition |
G>A |
All |
2978564 |
7.88 % |
| Transition |
T>C |
All |
14638732 |
38.73 % |
| Transition |
C>T |
All |
2196384 |
5.81 % |
| Transversion |
A>C |
All |
391453 |
1.04 % |
| Transversion |
C>A |
All |
1052815 |
2.79 % |
| Transversion |
T>G |
All |
486474 |
1.29 % |
| Transversion |
G>T |
All |
980327 |
2.59 % |
| Transversion |
A>T |
All |
687361 |
1.82 % |
| Transversion |
T>A |
All |
793476 |
2.10 % |
| Transversion |
C>G |
All |
401229 |
1.06 % |
| Transversion |
G>C |
All |
378434 |
1.00 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
920149 |
20.49 % |
| Transition |
G>A |
Passed |
535966 |
11.93 % |
| Transition |
T>C |
Passed |
1454461 |
32.38 % |
| Transition |
C>T |
Passed |
468483 |
10.43 % |
| Transversion |
A>C |
Passed |
132607 |
2.95 % |
| Transversion |
C>A |
Passed |
163453 |
3.64 % |
| Transversion |
T>G |
Passed |
150723 |
3.36 % |
| Transversion |
G>T |
Passed |
143762 |
3.20 % |
| Transversion |
A>T |
Passed |
110530 |
2.46 % |
| Transversion |
T>A |
Passed |
135574 |
3.02 % |
| Transversion |
C>G |
Passed |
139726 |
3.11 % |
| Transversion |
G>C |
Passed |
136229 |
3.03 % |
| |
|
|
|
|
| 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 |
6.31 |
32625884 |
5171569 |
| Passed |
3.04 |
3379059 |
1112604 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |