/cemt/variants/A83592_2_lane_gembs
BACK
SAMPLE A83592_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1169353442 |
921732124 |
78.82 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1169353442 |
100% |
1150974138 |
98.43 % |
18379304 |
1.57 % |
| |
|
|
|
|
|
|
| Passed |
925063331 |
79.11 % |
918825872 |
79.83 % |
6237459 |
0.67 % |
| Filtered |
244290111 |
20.89 % |
232148266 |
20.17 % |
12141845 |
1.31 % |
| |
|
|
|
|
|
|
| q20 |
214637681 |
87.86 % |
213363210 |
91.91 % |
1274471 |
10.50 % |
| q20,qd2 |
13725775 |
5.62 % |
3596525 |
1.55 % |
10129250 |
83.42 % |
| q20,mq40 |
9690875 |
3.97 % |
9596103 |
4.13 % |
94772 |
0.78 % |
| q20,qd2,mq40 |
2431878 |
1.00 % |
2305556 |
0.99 % |
126322 |
1.04 % |
| mq40 |
2050437 |
0.84 % |
1830642 |
0.79 % |
219795 |
1.81 % |
| qd2 |
1704432 |
0.70 % |
1418387 |
0.61 % |
286045 |
2.36 % |
| qd2,mq40 |
46548 |
0.02 % |
37843 |
0.02 % |
8705 |
0.07 % |
| qd2,fs60,mq40 |
1009 |
0.00 % |
0 |
0.00 % |
1009 |
0.01 % |
| qd2,fs60 |
594 |
0.00 % |
0 |
0.00 % |
594 |
0.00 % |
| fs60 |
370 |
0.00 % |
0 |
0.00 % |
370 |
0.00 % |
| fs60,mq40 |
256 |
0.00 % |
0 |
0.00 % |
256 |
0.00 % |
| q20,qd2,fs60 |
165 |
0.00 % |
0 |
0.00 % |
165 |
0.00 % |
| q20,qd2,fs60,mq40 |
90 |
0.00 % |
0 |
0.00 % |
90 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
7576659 |
37.73 % |
| Transition |
G>A |
All |
944041 |
4.70 % |
| Transition |
T>C |
All |
7603032 |
37.86 % |
| Transition |
C>T |
All |
948140 |
4.72 % |
| Transversion |
A>C |
All |
334414 |
1.67 % |
| Transversion |
C>A |
All |
455423 |
2.27 % |
| Transversion |
T>G |
All |
336829 |
1.68 % |
| Transversion |
G>T |
All |
441727 |
2.20 % |
| Transversion |
A>T |
All |
415823 |
2.07 % |
| Transversion |
T>A |
All |
425026 |
2.12 % |
| Transversion |
C>G |
All |
301319 |
1.50 % |
| Transversion |
G>C |
All |
299921 |
1.49 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
766127 |
19.24 % |
| Transition |
G>A |
Passed |
576464 |
14.48 % |
| Transition |
T>C |
Passed |
759226 |
19.07 % |
| Transition |
C>T |
Passed |
580557 |
14.58 % |
| Transversion |
A>C |
Passed |
167579 |
4.21 % |
| Transversion |
C>A |
Passed |
176727 |
4.44 % |
| Transversion |
T>G |
Passed |
168013 |
4.22 % |
| Transversion |
G>T |
Passed |
168532 |
4.23 % |
| Transversion |
A>T |
Passed |
149058 |
3.74 % |
| Transversion |
T>A |
Passed |
151998 |
3.82 % |
| Transversion |
C>G |
Passed |
158625 |
3.98 % |
| Transversion |
G>C |
Passed |
158341 |
3.98 % |
| |
|
|
|
|
| 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 |
5.67 |
17071872 |
3010482 |
| Passed |
2.07 |
2682374 |
1298873 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |