/CEMT/variants/A95342_2_lane_gembs
BACK
SAMPLE A95342_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1165972787 |
989016408 |
84.82 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1165972787 |
100% |
1151044914 |
98.72 % |
14927873 |
1.28 % |
| |
|
|
|
|
|
|
| Passed |
990724092 |
84.97 % |
986453302 |
85.70 % |
4270790 |
0.43 % |
| Filtered |
175248695 |
15.03 % |
164591612 |
14.30 % |
10657083 |
1.08 % |
| |
|
|
|
|
|
|
| q20 |
131065033 |
74.79 % |
129362453 |
78.60 % |
1702580 |
15.98 % |
| qd2 |
14213215 |
8.11 % |
13866399 |
8.42 % |
346816 |
3.25 % |
| q20,qd2 |
13820663 |
7.89 % |
5874475 |
3.57 % |
7946188 |
74.56 % |
| q20,mq40 |
9185677 |
5.24 % |
9060469 |
5.50 % |
125208 |
1.17 % |
| mq40 |
4676767 |
2.67 % |
4391792 |
2.67 % |
284975 |
2.67 % |
| q20,qd2,mq40 |
2134119 |
1.22 % |
1924641 |
1.17 % |
209478 |
1.97 % |
| qd2,mq40 |
131730 |
0.08 % |
111383 |
0.07 % |
20347 |
0.19 % |
| q20,qd2,fs60 |
6541 |
0.00 % |
0 |
0.00 % |
6541 |
0.06 % |
| qd2,fs60 |
5739 |
0.00 % |
0 |
0.00 % |
5739 |
0.05 % |
| fs60 |
5658 |
0.00 % |
0 |
0.00 % |
5658 |
0.05 % |
| qd2,fs60,mq40 |
2293 |
0.00 % |
0 |
0.00 % |
2293 |
0.02 % |
| fs60,mq40 |
761 |
0.00 % |
0 |
0.00 % |
761 |
0.01 % |
| q20,qd2,fs60,mq40 |
481 |
0.00 % |
0 |
0.00 % |
481 |
0.00 % |
| q20,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
4783080 |
23.35 % |
| Transition |
G>A |
All |
4292255 |
20.95 % |
| Transition |
T>C |
All |
4706816 |
22.98 % |
| Transition |
C>T |
All |
4294410 |
20.96 % |
| Transversion |
A>C |
All |
282088 |
1.38 % |
| Transversion |
C>A |
All |
351321 |
1.72 % |
| Transversion |
T>G |
All |
293355 |
1.43 % |
| Transversion |
G>T |
All |
349545 |
1.71 % |
| Transversion |
A>T |
All |
318483 |
1.55 % |
| Transversion |
T>A |
All |
318799 |
1.56 % |
| Transversion |
C>G |
All |
251132 |
1.23 % |
| Transversion |
G>C |
All |
243807 |
1.19 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
681494 |
18.44 % |
| Transition |
G>A |
Passed |
580901 |
15.71 % |
| Transition |
T>C |
Passed |
692588 |
18.74 % |
| Transition |
C>T |
Passed |
582331 |
15.75 % |
| Transversion |
A>C |
Passed |
151308 |
4.09 % |
| Transversion |
C>A |
Passed |
153463 |
4.15 % |
| Transversion |
T>G |
Passed |
151162 |
4.09 % |
| Transversion |
G>T |
Passed |
146823 |
3.97 % |
| Transversion |
A>T |
Passed |
120998 |
3.27 % |
| Transversion |
T>A |
Passed |
122179 |
3.31 % |
| Transversion |
C>G |
Passed |
156474 |
4.23 % |
| Transversion |
G>C |
Passed |
156951 |
4.25 % |
| |
|
|
|
|
| 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 |
7.51 |
18076561 |
2408530 |
| Passed |
2.19 |
2537314 |
1159358 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |