/cemt/variants/A77949_1_lane_gembs
BACK
SAMPLE A77949_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1177500794 |
969915146 |
82.37 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1177500794 |
100% |
1155913383 |
98.17 % |
21587411 |
1.83 % |
| |
|
|
|
|
|
|
| Passed |
973150686 |
82.65 % |
966619802 |
83.62 % |
6530884 |
0.67 % |
| Filtered |
204350108 |
17.35 % |
189293581 |
16.38 % |
15056527 |
1.55 % |
| |
|
|
|
|
|
|
| q20 |
167070294 |
81.76 % |
165805582 |
87.59 % |
1264712 |
8.40 % |
| q20,qd2 |
18095208 |
8.86 % |
5407820 |
2.86 % |
12687388 |
84.27 % |
| q20,mq40 |
11173809 |
5.47 % |
11045818 |
5.84 % |
127991 |
0.85 % |
| qd2 |
2856143 |
1.40 % |
2332185 |
1.23 % |
523958 |
3.48 % |
| q20,qd2,mq40 |
2831752 |
1.39 % |
2668056 |
1.41 % |
163696 |
1.09 % |
| mq40 |
2280451 |
1.12 % |
2001300 |
1.06 % |
279151 |
1.85 % |
| qd2,mq40 |
41266 |
0.02 % |
32820 |
0.02 % |
8446 |
0.06 % |
| qd2,fs60,mq40 |
545 |
0.00 % |
0 |
0.00 % |
545 |
0.00 % |
| qd2,fs60 |
240 |
0.00 % |
0 |
0.00 % |
240 |
0.00 % |
| fs60,mq40 |
208 |
0.00 % |
0 |
0.00 % |
208 |
0.00 % |
| fs60 |
108 |
0.00 % |
0 |
0.00 % |
108 |
0.00 % |
| q20,qd2,fs60,mq40 |
54 |
0.00 % |
0 |
0.00 % |
54 |
0.00 % |
| q20,qd2,fs60 |
27 |
0.00 % |
0 |
0.00 % |
27 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
8466105 |
36.05 % |
| Transition |
G>A |
All |
1035415 |
4.41 % |
| Transition |
T>C |
All |
8436665 |
35.92 % |
| Transition |
C>T |
All |
1038921 |
4.42 % |
| Transversion |
A>C |
All |
348317 |
1.48 % |
| Transversion |
C>A |
All |
1099122 |
4.68 % |
| Transversion |
T>G |
All |
351846 |
1.50 % |
| Transversion |
G>T |
All |
902903 |
3.84 % |
| Transversion |
A>T |
All |
568118 |
2.42 % |
| Transversion |
T>A |
All |
591721 |
2.52 % |
| Transversion |
C>G |
All |
326604 |
1.39 % |
| Transversion |
G>C |
All |
318612 |
1.36 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
919733 |
20.20 % |
| Transition |
G>A |
Passed |
570898 |
12.54 % |
| Transition |
T>C |
Passed |
869203 |
19.09 % |
| Transition |
C>T |
Passed |
570210 |
12.53 % |
| Transversion |
A>C |
Passed |
165403 |
3.63 % |
| Transversion |
C>A |
Passed |
363799 |
7.99 % |
| Transversion |
T>G |
Passed |
168230 |
3.70 % |
| Transversion |
G>T |
Passed |
284428 |
6.25 % |
| Transversion |
A>T |
Passed |
156720 |
3.44 % |
| Transversion |
T>A |
Passed |
165599 |
3.64 % |
| Transversion |
C>G |
Passed |
160080 |
3.52 % |
| Transversion |
G>C |
Passed |
157993 |
3.47 % |
| |
|
|
|
|
| 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 |
4.21 |
18977106 |
4507243 |
| Passed |
1.81 |
2930044 |
1622252 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |