/EXTERNAL DEEP/variants/K009022_K009023_K009024_3_lane_gembs
BACK
SAMPLE K009022_K009023_K009024_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1167749802 |
670283901 |
57.40 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1167749802 |
100% |
1131597956 |
96.90 % |
36151846 |
3.10 % |
| |
|
|
|
|
|
|
| Passed |
676365662 |
57.92 % |
666536295 |
58.90 % |
9829367 |
1.45 % |
| Filtered |
491384140 |
42.08 % |
465061661 |
41.10 % |
26322479 |
3.89 % |
| |
|
|
|
|
|
|
| q20 |
436723216 |
88.88 % |
429554750 |
92.37 % |
7168466 |
27.23 % |
| q20,qd2 |
34730866 |
7.07 % |
16456087 |
3.54 % |
18274779 |
69.43 % |
| q20,mq40 |
10328813 |
2.10 % |
10110595 |
2.17 % |
218218 |
0.83 % |
| qd2 |
5139431 |
1.05 % |
4911812 |
1.06 % |
227619 |
0.86 % |
| q20,qd2,mq40 |
3569905 |
0.73 % |
3378909 |
0.73 % |
190996 |
0.73 % |
| mq40 |
847640 |
0.17 % |
614480 |
0.13 % |
233160 |
0.89 % |
| qd2,mq40 |
42668 |
0.01 % |
35028 |
0.01 % |
7640 |
0.03 % |
| qd2,fs60,mq40 |
675 |
0.00 % |
0 |
0.00 % |
675 |
0.00 % |
| qd2,fs60 |
274 |
0.00 % |
0 |
0.00 % |
274 |
0.00 % |
| fs60,mq40 |
265 |
0.00 % |
0 |
0.00 % |
265 |
0.00 % |
| fs60 |
162 |
0.00 % |
0 |
0.00 % |
162 |
0.00 % |
| q20,qd2,fs60,mq40 |
148 |
0.00 % |
0 |
0.00 % |
148 |
0.00 % |
| q20,qd2,fs60 |
77 |
0.00 % |
0 |
0.00 % |
77 |
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 |
11591705 |
30.39 % |
| Transition |
G>A |
All |
2493657 |
6.54 % |
| Transition |
T>C |
All |
12602588 |
33.04 % |
| Transition |
C>T |
All |
2065280 |
5.41 % |
| Transversion |
A>C |
All |
632908 |
1.66 % |
| Transversion |
C>A |
All |
2358045 |
6.18 % |
| Transversion |
T>G |
All |
719963 |
1.89 % |
| Transversion |
G>T |
All |
2334114 |
6.12 % |
| Transversion |
A>T |
All |
1034807 |
2.71 % |
| Transversion |
T>A |
All |
1090150 |
2.86 % |
| Transversion |
C>G |
All |
621679 |
1.63 % |
| Transversion |
G>C |
All |
598515 |
1.57 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
858118 |
19.31 % |
| Transition |
G>A |
Passed |
540439 |
12.16 % |
| Transition |
T>C |
Passed |
1199823 |
27.00 % |
| Transition |
C>T |
Passed |
480420 |
10.81 % |
| Transversion |
A>C |
Passed |
145845 |
3.28 % |
| Transversion |
C>A |
Passed |
252379 |
5.68 % |
| Transversion |
T>G |
Passed |
157419 |
3.54 % |
| Transversion |
G>T |
Passed |
233596 |
5.26 % |
| Transversion |
A>T |
Passed |
126322 |
2.84 % |
| Transversion |
T>A |
Passed |
145572 |
3.28 % |
| Transversion |
C>G |
Passed |
151392 |
3.41 % |
| Transversion |
G>C |
Passed |
152449 |
3.43 % |
| |
|
|
|
|
| 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 |
3.06 |
28753230 |
9390181 |
| Passed |
2.26 |
3078800 |
1364974 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |