/CEMT/variants/B33202_1_lane_gembs
BACK
SAMPLE B33202_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1169900416 |
903994526 |
77.27 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1169900416 |
100% |
1150683058 |
98.36 % |
19217358 |
1.64 % |
| |
|
|
|
|
|
|
| Passed |
907519018 |
77.57 % |
901262297 |
78.32 % |
6256721 |
0.69 % |
| Filtered |
262381398 |
22.43 % |
249420761 |
21.68 % |
12960637 |
1.43 % |
| |
|
|
|
|
|
|
| q20 |
228820180 |
87.21 % |
226955713 |
90.99 % |
1864467 |
14.39 % |
| q20,qd2 |
14872364 |
5.67 % |
4564091 |
1.83 % |
10308273 |
79.54 % |
| q20,mq40 |
11016017 |
4.20 % |
10897030 |
4.37 % |
118987 |
0.92 % |
| mq40 |
2603358 |
0.99 % |
2356428 |
0.94 % |
246930 |
1.91 % |
| qd2 |
2512494 |
0.96 % |
2253806 |
0.90 % |
258688 |
2.00 % |
| q20,qd2,mq40 |
2501359 |
0.95 % |
2349839 |
0.94 % |
151520 |
1.17 % |
| qd2,mq40 |
53143 |
0.02 % |
43854 |
0.02 % |
9289 |
0.07 % |
| qd2,fs60,mq40 |
829 |
0.00 % |
0 |
0.00 % |
829 |
0.01 % |
| qd2,fs60 |
544 |
0.00 % |
0 |
0.00 % |
544 |
0.00 % |
| q20,qd2,fs60 |
400 |
0.00 % |
0 |
0.00 % |
400 |
0.00 % |
| fs60 |
310 |
0.00 % |
0 |
0.00 % |
310 |
0.00 % |
| fs60,mq40 |
273 |
0.00 % |
0 |
0.00 % |
273 |
0.00 % |
| q20,qd2,fs60,mq40 |
127 |
0.00 % |
0 |
0.00 % |
127 |
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 |
7806987 |
37.27 % |
| Transition |
G>A |
All |
1036942 |
4.95 % |
| Transition |
T>C |
All |
7842943 |
37.44 % |
| Transition |
C>T |
All |
1042141 |
4.98 % |
| Transversion |
A>C |
All |
420674 |
2.01 % |
| Transversion |
C>A |
All |
457789 |
2.19 % |
| Transversion |
T>G |
All |
421865 |
2.01 % |
| Transversion |
G>T |
All |
448416 |
2.14 % |
| Transversion |
A>T |
All |
379523 |
1.81 % |
| Transversion |
T>A |
All |
382928 |
1.83 % |
| Transversion |
C>G |
All |
353020 |
1.69 % |
| Transversion |
G>C |
All |
352029 |
1.68 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
737190 |
19.60 % |
| Transition |
G>A |
Passed |
543015 |
14.44 % |
| Transition |
T>C |
Passed |
730678 |
19.42 % |
| Transition |
C>T |
Passed |
541403 |
14.39 % |
| Transversion |
A>C |
Passed |
159558 |
4.24 % |
| Transversion |
C>A |
Passed |
164224 |
4.37 % |
| Transversion |
T>G |
Passed |
160044 |
4.25 % |
| Transversion |
G>T |
Passed |
155935 |
4.15 % |
| Transversion |
A>T |
Passed |
130368 |
3.47 % |
| Transversion |
T>A |
Passed |
132044 |
3.51 % |
| Transversion |
C>G |
Passed |
153565 |
4.08 % |
| Transversion |
G>C |
Passed |
153679 |
4.09 % |
| |
|
|
|
|
| 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 |
5.51 |
17729013 |
3216244 |
| Passed |
2.11 |
2552286 |
1209417 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |