/CEMT/variants/A50423_A50425_4_lane_gembs
BACK
SAMPLE A50423_A50425_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1132293798 |
248882905 |
21.98 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1132293798 |
100% |
1106690145 |
97.74 % |
25603653 |
2.26 % |
| |
|
|
|
|
|
|
| Passed |
254237801 |
22.45 % |
247665272 |
22.38 % |
6572529 |
2.59 % |
| Filtered |
878055997 |
77.55 % |
859024873 |
77.62 % |
19031124 |
7.49 % |
| |
|
|
|
|
|
|
| q20 |
789608696 |
89.93 % |
782597549 |
91.10 % |
7011147 |
36.84 % |
| q20,qd2 |
70720528 |
8.05 % |
59087328 |
6.88 % |
11633200 |
61.13 % |
| q20,mq40 |
10872754 |
1.24 % |
10726121 |
1.25 % |
146633 |
0.77 % |
| q20,qd2,mq40 |
5080570 |
0.58 % |
4976028 |
0.58 % |
104542 |
0.55 % |
| qd2 |
1411447 |
0.16 % |
1368518 |
0.16 % |
42929 |
0.23 % |
| mq40 |
339934 |
0.04 % |
251698 |
0.03 % |
88236 |
0.46 % |
| qd2,mq40 |
21303 |
0.00 % |
17631 |
0.00 % |
3672 |
0.02 % |
| qd2,fs60,mq40 |
351 |
0.00 % |
0 |
0.00 % |
351 |
0.00 % |
| qd2,fs60 |
187 |
0.00 % |
0 |
0.00 % |
187 |
0.00 % |
| fs60,mq40 |
103 |
0.00 % |
0 |
0.00 % |
103 |
0.00 % |
| q20,qd2,fs60,mq40 |
48 |
0.00 % |
0 |
0.00 % |
48 |
0.00 % |
| fs60 |
40 |
0.00 % |
0 |
0.00 % |
40 |
0.00 % |
| q20,qd2,fs60 |
36 |
0.00 % |
0 |
0.00 % |
36 |
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 |
7014369 |
24.74 % |
| Transition |
G>A |
All |
1576566 |
5.56 % |
| Transition |
T>C |
All |
5768809 |
20.35 % |
| Transition |
C>T |
All |
1647289 |
5.81 % |
| Transversion |
A>C |
All |
771558 |
2.72 % |
| Transversion |
C>A |
All |
2236554 |
7.89 % |
| Transversion |
T>G |
All |
907865 |
3.20 % |
| Transversion |
G>T |
All |
2153646 |
7.60 % |
| Transversion |
A>T |
All |
2496311 |
8.81 % |
| Transversion |
T>A |
All |
2612995 |
9.22 % |
| Transversion |
C>G |
All |
628885 |
2.22 % |
| Transversion |
G>C |
All |
532997 |
1.88 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
261299 |
17.07 % |
| Transition |
G>A |
Passed |
229142 |
14.97 % |
| Transition |
T>C |
Passed |
248779 |
16.25 % |
| Transition |
C>T |
Passed |
232246 |
15.17 % |
| Transversion |
A>C |
Passed |
65487 |
4.28 % |
| Transversion |
C>A |
Passed |
78016 |
5.10 % |
| Transversion |
T>G |
Passed |
67595 |
4.42 % |
| Transversion |
G>T |
Passed |
77120 |
5.04 % |
| Transversion |
A>T |
Passed |
76996 |
5.03 % |
| Transversion |
T>A |
Passed |
77671 |
5.07 % |
| Transversion |
C>G |
Passed |
58673 |
3.83 % |
| Transversion |
G>C |
Passed |
57958 |
3.79 % |
| |
|
|
|
|
| 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 |
1.30 |
16007033 |
12340811 |
| Passed |
1.74 |
971466 |
559516 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |