/CEMT/variants/B19820_2_lane_gembs
BACK
SAMPLE B19820_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1165174149 |
1053599813 |
90.42 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1165174149 |
100% |
1152026285 |
98.87 % |
13147864 |
1.13 % |
| |
|
|
|
|
|
|
| Passed |
1054823760 |
90.53 % |
1050995698 |
91.23 % |
3828062 |
0.36 % |
| Filtered |
110350389 |
9.47 % |
101030587 |
8.77 % |
9319802 |
0.88 % |
| |
|
|
|
|
|
|
| q20 |
79678451 |
72.20 % |
78355262 |
77.56 % |
1323189 |
14.20 % |
| q20,qd2 |
11297273 |
10.24 % |
4340143 |
4.30 % |
6957130 |
74.65 % |
| q20,mq40 |
9239707 |
8.37 % |
9103558 |
9.01 % |
136149 |
1.46 % |
| mq40 |
4871760 |
4.41 % |
4557420 |
4.51 % |
314340 |
3.37 % |
| qd2 |
2921092 |
2.65 % |
2595084 |
2.57 % |
326008 |
3.50 % |
| q20,qd2,mq40 |
2186298 |
1.98 % |
1958528 |
1.94 % |
227770 |
2.44 % |
| qd2,mq40 |
143571 |
0.13 % |
120592 |
0.12 % |
22979 |
0.25 % |
| q20,qd2,fs60 |
3213 |
0.00 % |
0 |
0.00 % |
3213 |
0.03 % |
| fs60 |
3161 |
0.00 % |
0 |
0.00 % |
3161 |
0.03 % |
| qd2,fs60 |
2358 |
0.00 % |
0 |
0.00 % |
2358 |
0.03 % |
| qd2,fs60,mq40 |
2134 |
0.00 % |
0 |
0.00 % |
2134 |
0.02 % |
| fs60,mq40 |
945 |
0.00 % |
0 |
0.00 % |
945 |
0.01 % |
| q20,qd2,fs60,mq40 |
410 |
0.00 % |
0 |
0.00 % |
410 |
0.00 % |
| q20,fs60,mq40 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| q20,fs60 |
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 |
4045981 |
25.43 % |
| Transition |
G>A |
All |
2715052 |
17.07 % |
| Transition |
T>C |
All |
3983589 |
25.04 % |
| Transition |
C>T |
All |
2737651 |
17.21 % |
| Transversion |
A>C |
All |
275285 |
1.73 % |
| Transversion |
C>A |
All |
359271 |
2.26 % |
| Transversion |
T>G |
All |
285813 |
1.80 % |
| Transversion |
G>T |
All |
357929 |
2.25 % |
| Transversion |
A>T |
All |
328305 |
2.06 % |
| Transversion |
T>A |
All |
329228 |
2.07 % |
| Transversion |
C>G |
All |
247922 |
1.56 % |
| Transversion |
G>C |
All |
242428 |
1.52 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
692367 |
18.11 % |
| Transition |
G>A |
Passed |
604437 |
15.81 % |
| Transition |
T>C |
Passed |
693556 |
18.14 % |
| Transition |
C>T |
Passed |
605446 |
15.84 % |
| Transversion |
A>C |
Passed |
159880 |
4.18 % |
| Transversion |
C>A |
Passed |
163745 |
4.28 % |
| Transversion |
T>G |
Passed |
160861 |
4.21 % |
| Transversion |
G>T |
Passed |
156738 |
4.10 % |
| Transversion |
A>T |
Passed |
129629 |
3.39 % |
| Transversion |
T>A |
Passed |
130830 |
3.42 % |
| Transversion |
C>G |
Passed |
162705 |
4.26 % |
| Transversion |
G>C |
Passed |
162300 |
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 |
5.56 |
13482273 |
2426181 |
| Passed |
2.12 |
2595806 |
1226688 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |