/CEMT/variants/A54772_3_lane_gembs
BACK
SAMPLE A54772_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1161136033 |
685432184 |
59.03 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1161136033 |
100% |
1138649979 |
98.06 % |
22486054 |
1.94 % |
| |
|
|
|
|
|
|
| Passed |
688670936 |
59.31 % |
683224995 |
60.00 % |
5445941 |
0.79 % |
| Filtered |
472465097 |
40.69 % |
455424984 |
40.00 % |
17040113 |
2.47 % |
| |
|
|
|
|
|
|
| q20 |
416181809 |
88.09 % |
411557787 |
90.37 % |
4624022 |
27.14 % |
| q20,qd2 |
25895416 |
5.48 % |
14384277 |
3.16 % |
11511139 |
67.55 % |
| qd2 |
13439857 |
2.84 % |
13203379 |
2.90 % |
236478 |
1.39 % |
| q20,mq40 |
11514776 |
2.44 % |
11294461 |
2.48 % |
220315 |
1.29 % |
| q20,qd2,mq40 |
3456267 |
0.73 % |
3216392 |
0.71 % |
239875 |
1.41 % |
| mq40 |
1887098 |
0.40 % |
1710229 |
0.38 % |
176869 |
1.04 % |
| qd2,mq40 |
69601 |
0.01 % |
58459 |
0.01 % |
11142 |
0.07 % |
| q20,qd2,fs60 |
6769 |
0.00 % |
0 |
0.00 % |
6769 |
0.04 % |
| fs60 |
6552 |
0.00 % |
0 |
0.00 % |
6552 |
0.04 % |
| qd2,fs60 |
4949 |
0.00 % |
0 |
0.00 % |
4949 |
0.03 % |
| qd2,fs60,mq40 |
1370 |
0.00 % |
0 |
0.00 % |
1370 |
0.01 % |
| fs60,mq40 |
403 |
0.00 % |
0 |
0.00 % |
403 |
0.00 % |
| q20,qd2,fs60,mq40 |
217 |
0.00 % |
0 |
0.00 % |
217 |
0.00 % |
| q20,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| q20,fs60,mq40 |
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 |
7671173 |
30.32 % |
| Transition |
G>A |
All |
2222283 |
8.78 % |
| Transition |
T>C |
All |
6123692 |
24.20 % |
| Transition |
C>T |
All |
2301934 |
9.10 % |
| Transversion |
A>C |
All |
429402 |
1.70 % |
| Transversion |
C>A |
All |
1431725 |
5.66 % |
| Transversion |
T>G |
All |
508865 |
2.01 % |
| Transversion |
G>T |
All |
1373543 |
5.43 % |
| Transversion |
A>T |
All |
1180200 |
4.66 % |
| Transversion |
T>A |
All |
1237774 |
4.89 % |
| Transversion |
C>G |
All |
450103 |
1.78 % |
| Transversion |
G>C |
All |
372722 |
1.47 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
591886 |
19.13 % |
| Transition |
G>A |
Passed |
463073 |
14.96 % |
| Transition |
T>C |
Passed |
538323 |
17.40 % |
| Transition |
C>T |
Passed |
466489 |
15.07 % |
| Transversion |
A>C |
Passed |
125284 |
4.05 % |
| Transversion |
C>A |
Passed |
144328 |
4.66 % |
| Transversion |
T>G |
Passed |
128016 |
4.14 % |
| Transversion |
G>T |
Passed |
141942 |
4.59 % |
| Transversion |
A>T |
Passed |
128609 |
4.16 % |
| Transversion |
T>A |
Passed |
130863 |
4.23 % |
| Transversion |
C>G |
Passed |
118523 |
3.83 % |
| Transversion |
G>C |
Passed |
117246 |
3.79 % |
| |
|
|
|
|
| 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 |
2.62 |
18319082 |
6984334 |
| Passed |
1.99 |
2059771 |
1034811 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |