/cemt/variants/A70096_3_lane_gembs
BACK
SAMPLE A70096_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170817610 |
1065101016 |
90.97 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170817610 |
100% |
1152520391 |
98.44 % |
18297219 |
1.56 % |
| |
|
|
|
|
|
|
| Passed |
1066906705 |
91.12 % |
1061905042 |
92.14 % |
5001663 |
0.47 % |
| Filtered |
103910905 |
8.88 % |
90615349 |
7.86 % |
13295556 |
1.25 % |
| |
|
|
|
|
|
|
| q20 |
72417742 |
69.69 % |
71777424 |
79.21 % |
640318 |
4.82 % |
| q20,qd2 |
14602929 |
14.05 % |
2947317 |
3.25 % |
11655612 |
87.67 % |
| q20,mq40 |
9995940 |
9.62 % |
9901877 |
10.93 % |
94063 |
0.71 % |
| mq40 |
2812693 |
2.71 % |
2563244 |
2.83 % |
249449 |
1.88 % |
| q20,qd2,mq40 |
2367262 |
2.28 % |
2224626 |
2.46 % |
142636 |
1.07 % |
| qd2 |
1663750 |
1.60 % |
1162073 |
1.28 % |
501677 |
3.77 % |
| qd2,mq40 |
48806 |
0.05 % |
38788 |
0.04 % |
10018 |
0.08 % |
| qd2,fs60,mq40 |
761 |
0.00 % |
0 |
0.00 % |
761 |
0.01 % |
| qd2,fs60 |
390 |
0.00 % |
0 |
0.00 % |
390 |
0.00 % |
| fs60,mq40 |
277 |
0.00 % |
0 |
0.00 % |
277 |
0.00 % |
| fs60 |
215 |
0.00 % |
0 |
0.00 % |
215 |
0.00 % |
| q20,qd2,fs60,mq40 |
71 |
0.00 % |
0 |
0.00 % |
71 |
0.00 % |
| q20,qd2,fs60 |
67 |
0.00 % |
0 |
0.00 % |
67 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
7577715 |
37.95 % |
| Transition |
G>A |
All |
981677 |
4.92 % |
| Transition |
T>C |
All |
7675104 |
38.44 % |
| Transition |
C>T |
All |
984611 |
4.93 % |
| Transversion |
A>C |
All |
261866 |
1.31 % |
| Transversion |
C>A |
All |
433066 |
2.17 % |
| Transversion |
T>G |
All |
267480 |
1.34 % |
| Transversion |
G>T |
All |
419757 |
2.10 % |
| Transversion |
A>T |
All |
430871 |
2.16 % |
| Transversion |
T>A |
All |
440689 |
2.21 % |
| Transversion |
C>G |
All |
248592 |
1.24 % |
| Transversion |
G>C |
All |
246172 |
1.23 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
936853 |
21.12 % |
| Transition |
G>A |
Passed |
628518 |
14.17 % |
| Transition |
T>C |
Passed |
910876 |
20.53 % |
| Transition |
C>T |
Passed |
627418 |
14.14 % |
| Transversion |
A>C |
Passed |
170062 |
3.83 % |
| Transversion |
C>A |
Passed |
178320 |
4.02 % |
| Transversion |
T>G |
Passed |
171189 |
3.86 % |
| Transversion |
G>T |
Passed |
169883 |
3.83 % |
| Transversion |
A>T |
Passed |
150704 |
3.40 % |
| Transversion |
T>A |
Passed |
154360 |
3.48 % |
| Transversion |
C>G |
Passed |
169255 |
3.81 % |
| Transversion |
G>C |
Passed |
169137 |
3.81 % |
| |
|
|
|
|
| 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 |
6.26 |
17219107 |
2748493 |
| Passed |
2.33 |
3103665 |
1332910 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |