/CEMT/variants/A75623_1_lane_gembs
BACK
SAMPLE A75623_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1176886597 |
1011366515 |
85.94 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1176886597 |
100% |
1157366740 |
98.34 % |
19519857 |
1.66 % |
| |
|
|
|
|
|
|
| Passed |
1013965759 |
86.16 % |
1008219828 |
87.11 % |
5745931 |
0.57 % |
| Filtered |
162920838 |
13.84 % |
149146912 |
12.89 % |
13773926 |
1.36 % |
| |
|
|
|
|
|
|
| q20 |
128752305 |
79.03 % |
127740534 |
85.65 % |
1011771 |
7.35 % |
| q20,qd2 |
15458688 |
9.49 % |
3701661 |
2.48 % |
11757027 |
85.36 % |
| q20,mq40 |
11279712 |
6.92 % |
11164084 |
7.49 % |
115628 |
0.84 % |
| mq40 |
2874194 |
1.76 % |
2616243 |
1.75 % |
257951 |
1.87 % |
| q20,qd2,mq40 |
2557793 |
1.57 % |
2398535 |
1.61 % |
159258 |
1.16 % |
| qd2 |
1943318 |
1.19 % |
1482697 |
0.99 % |
460621 |
3.34 % |
| qd2,mq40 |
53320 |
0.03 % |
43158 |
0.03 % |
10162 |
0.07 % |
| qd2,fs60,mq40 |
670 |
0.00 % |
0 |
0.00 % |
670 |
0.00 % |
| fs60,mq40 |
313 |
0.00 % |
0 |
0.00 % |
313 |
0.00 % |
| qd2,fs60 |
278 |
0.00 % |
0 |
0.00 % |
278 |
0.00 % |
| fs60 |
145 |
0.00 % |
0 |
0.00 % |
145 |
0.00 % |
| q20,qd2,fs60,mq40 |
60 |
0.00 % |
0 |
0.00 % |
60 |
0.00 % |
| q20,qd2,fs60 |
42 |
0.00 % |
0 |
0.00 % |
42 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
7942853 |
37.39 % |
| Transition |
G>A |
All |
940487 |
4.43 % |
| Transition |
T>C |
All |
8034262 |
37.82 % |
| Transition |
C>T |
All |
947627 |
4.46 % |
| Transversion |
A>C |
All |
353378 |
1.66 % |
| Transversion |
C>A |
All |
512327 |
2.41 % |
| Transversion |
T>G |
All |
357548 |
1.68 % |
| Transversion |
G>T |
All |
504078 |
2.37 % |
| Transversion |
A>T |
All |
503999 |
2.37 % |
| Transversion |
T>A |
All |
513791 |
2.42 % |
| Transversion |
C>G |
All |
318641 |
1.50 % |
| Transversion |
G>C |
All |
315657 |
1.49 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
944495 |
21.77 % |
| Transition |
G>A |
Passed |
593901 |
13.69 % |
| Transition |
T>C |
Passed |
852517 |
19.65 % |
| Transition |
C>T |
Passed |
592843 |
13.67 % |
| Transversion |
A>C |
Passed |
178123 |
4.11 % |
| Transversion |
C>A |
Passed |
179938 |
4.15 % |
| Transversion |
T>G |
Passed |
180550 |
4.16 % |
| Transversion |
G>T |
Passed |
171344 |
3.95 % |
| Transversion |
A>T |
Passed |
152468 |
3.51 % |
| Transversion |
T>A |
Passed |
156329 |
3.60 % |
| Transversion |
C>G |
Passed |
168297 |
3.88 % |
| Transversion |
G>C |
Passed |
167516 |
3.86 % |
| |
|
|
|
|
| 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 |
5.29 |
17865229 |
3379419 |
| Passed |
2.20 |
2983756 |
1354565 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |