/cemt/variants/A54779_3_lane_gembs
BACK
SAMPLE A54779_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1166384695 |
639547559 |
54.83 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1166384695 |
100% |
1143605976 |
98.05 % |
22778719 |
1.95 % |
| |
|
|
|
|
|
|
| Passed |
643003493 |
55.13 % |
637458858 |
55.74 % |
5544635 |
0.86 % |
| Filtered |
523381202 |
44.87 % |
506147118 |
44.26 % |
17234084 |
2.68 % |
| |
|
|
|
|
|
|
| q20 |
461349128 |
88.15 % |
456602117 |
90.21 % |
4747011 |
27.54 % |
| q20,qd2 |
27465660 |
5.25 % |
15900386 |
3.14 % |
11565274 |
67.11 % |
| qd2 |
17397567 |
3.32 % |
17149441 |
3.39 % |
248126 |
1.44 % |
| q20,mq40 |
11715050 |
2.24 % |
11496902 |
2.27 % |
218148 |
1.27 % |
| q20,qd2,mq40 |
3577966 |
0.68 % |
3338225 |
0.66 % |
239741 |
1.39 % |
| mq40 |
1763869 |
0.34 % |
1592679 |
0.31 % |
171190 |
0.99 % |
| qd2,mq40 |
79383 |
0.02 % |
67368 |
0.01 % |
12015 |
0.07 % |
| q20,qd2,fs60 |
11169 |
0.00 % |
0 |
0.00 % |
11169 |
0.06 % |
| fs60 |
10396 |
0.00 % |
0 |
0.00 % |
10396 |
0.06 % |
| qd2,fs60 |
8616 |
0.00 % |
0 |
0.00 % |
8616 |
0.05 % |
| qd2,fs60,mq40 |
1590 |
0.00 % |
0 |
0.00 % |
1590 |
0.01 % |
| fs60,mq40 |
515 |
0.00 % |
0 |
0.00 % |
515 |
0.00 % |
| q20,qd2,fs60,mq40 |
280 |
0.00 % |
0 |
0.00 % |
280 |
0.00 % |
| q20,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
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 |
7515040 |
29.29 % |
| Transition |
G>A |
All |
2208034 |
8.61 % |
| Transition |
T>C |
All |
6157505 |
24.00 % |
| Transition |
C>T |
All |
2277649 |
8.88 % |
| Transversion |
A>C |
All |
442010 |
1.72 % |
| Transversion |
C>A |
All |
1455191 |
5.67 % |
| Transversion |
T>G |
All |
523839 |
2.04 % |
| Transversion |
G>T |
All |
1388380 |
5.41 % |
| Transversion |
A>T |
All |
1378262 |
5.37 % |
| Transversion |
T>A |
All |
1449623 |
5.65 % |
| Transversion |
C>G |
All |
467317 |
1.82 % |
| Transversion |
G>C |
All |
390544 |
1.52 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
547846 |
18.60 % |
| Transition |
G>A |
Passed |
441258 |
14.98 % |
| Transition |
T>C |
Passed |
508250 |
17.26 % |
| Transition |
C>T |
Passed |
444453 |
15.09 % |
| Transversion |
A>C |
Passed |
118937 |
4.04 % |
| Transversion |
C>A |
Passed |
142835 |
4.85 % |
| Transversion |
T>G |
Passed |
121595 |
4.13 % |
| Transversion |
G>T |
Passed |
138858 |
4.71 % |
| Transversion |
A>T |
Passed |
126724 |
4.30 % |
| Transversion |
T>A |
Passed |
130486 |
4.43 % |
| Transversion |
C>G |
Passed |
112638 |
3.82 % |
| Transversion |
G>C |
Passed |
111208 |
3.78 % |
| |
|
|
|
|
| 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 |
2.42 |
18158228 |
7495166 |
| Passed |
1.94 |
1941807 |
1003281 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |