/cemt/variants/A59694_3_lane_gembs
BACK
SAMPLE A59694_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1159209736 |
1055541523 |
91.06 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1159209736 |
100% |
1147020941 |
98.95 % |
12188795 |
1.05 % |
| |
|
|
|
|
|
|
| Passed |
1056150777 |
91.11 % |
1052452128 |
91.76 % |
3698649 |
0.35 % |
| Filtered |
103058959 |
8.89 % |
94568813 |
8.24 % |
8490146 |
0.80 % |
| |
|
|
|
|
|
|
| q20 |
69448353 |
67.39 % |
68375991 |
72.30 % |
1072362 |
12.63 % |
| q20,mq40 |
11287691 |
10.95 % |
11051270 |
11.69 % |
236421 |
2.78 % |
| q20,qd2 |
11129768 |
10.80 % |
4829749 |
5.11 % |
6300019 |
74.20 % |
| qd2 |
5055518 |
4.91 % |
4703057 |
4.97 % |
352461 |
4.15 % |
| q20,qd2,mq40 |
3074931 |
2.98 % |
2787068 |
2.95 % |
287863 |
3.39 % |
| mq40 |
2998621 |
2.91 % |
2771541 |
2.93 % |
227080 |
2.67 % |
| qd2,mq40 |
60177 |
0.06 % |
50137 |
0.05 % |
10040 |
0.12 % |
| qd2,fs60,mq40 |
1051 |
0.00 % |
0 |
0.00 % |
1051 |
0.01 % |
| fs60 |
891 |
0.00 % |
0 |
0.00 % |
891 |
0.01 % |
| q20,qd2,fs60 |
857 |
0.00 % |
0 |
0.00 % |
857 |
0.01 % |
| qd2,fs60 |
637 |
0.00 % |
0 |
0.00 % |
637 |
0.01 % |
| fs60,mq40 |
368 |
0.00 % |
0 |
0.00 % |
368 |
0.00 % |
| q20,qd2,fs60,mq40 |
88 |
0.00 % |
0 |
0.00 % |
88 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
3436227 |
24.63 % |
| Transition |
G>A |
All |
1078959 |
7.73 % |
| Transition |
T>C |
All |
3437353 |
24.64 % |
| Transition |
C>T |
All |
1076651 |
7.72 % |
| Transversion |
A>C |
All |
467776 |
3.35 % |
| Transversion |
C>A |
All |
775399 |
5.56 % |
| Transversion |
T>G |
All |
462662 |
3.32 % |
| Transversion |
G>T |
All |
796377 |
5.71 % |
| Transversion |
A>T |
All |
894002 |
6.41 % |
| Transversion |
T>A |
All |
867292 |
6.22 % |
| Transversion |
C>G |
All |
326832 |
2.34 % |
| Transversion |
G>C |
All |
329904 |
2.36 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
725394 |
16.80 % |
| Transition |
G>A |
Passed |
640805 |
14.84 % |
| Transition |
T>C |
Passed |
730065 |
16.91 % |
| Transition |
C>T |
Passed |
642244 |
14.88 % |
| Transversion |
A>C |
Passed |
213630 |
4.95 % |
| Transversion |
C>A |
Passed |
214460 |
4.97 % |
| Transversion |
T>G |
Passed |
211875 |
4.91 % |
| Transversion |
G>T |
Passed |
212298 |
4.92 % |
| Transversion |
A>T |
Passed |
191978 |
4.45 % |
| Transversion |
T>A |
Passed |
191634 |
4.44 % |
| Transversion |
C>G |
Passed |
170805 |
3.96 % |
| Transversion |
G>C |
Passed |
171833 |
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 |
1.84 |
9029190 |
4920244 |
| Passed |
1.73 |
2738508 |
1578513 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |