/cemt/variants/K005737_0_lane_gembs
BACK
SAMPLE K005737_0_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1171553414 |
610032276 |
52.07 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1171553414 |
100% |
1147789411 |
97.97 % |
23764003 |
2.03 % |
| |
|
|
|
|
|
|
| Passed |
615133206 |
52.51 % |
607528746 |
52.93 % |
7604460 |
1.24 % |
| Filtered |
556420208 |
47.49 % |
540260665 |
47.07 % |
16159543 |
2.63 % |
| |
|
|
|
|
|
|
| q20 |
511911408 |
92.00 % |
507751842 |
93.98 % |
4159566 |
25.74 % |
| q20,qd2 |
24570287 |
4.42 % |
13372252 |
2.48 % |
11198035 |
69.30 % |
| q20,mq40 |
12169377 |
2.19 % |
12020516 |
2.22 % |
148861 |
0.92 % |
| q20,qd2,mq40 |
3259929 |
0.59 % |
3093731 |
0.57 % |
166198 |
1.03 % |
| qd2 |
2375299 |
0.43 % |
2125855 |
0.39 % |
249444 |
1.54 % |
| mq40 |
2086616 |
0.38 % |
1859077 |
0.34 % |
227539 |
1.41 % |
| qd2,mq40 |
45500 |
0.01 % |
37392 |
0.01 % |
8108 |
0.05 % |
| qd2,fs60,mq40 |
785 |
0.00 % |
0 |
0.00 % |
785 |
0.00 % |
| qd2,fs60 |
423 |
0.00 % |
0 |
0.00 % |
423 |
0.00 % |
| fs60,mq40 |
171 |
0.00 % |
0 |
0.00 % |
171 |
0.00 % |
| q20,qd2,fs60 |
152 |
0.00 % |
0 |
0.00 % |
152 |
0.00 % |
| fs60 |
151 |
0.00 % |
0 |
0.00 % |
151 |
0.00 % |
| q20,qd2,fs60,mq40 |
108 |
0.00 % |
0 |
0.00 % |
108 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
9439750 |
36.64 % |
| Transition |
G>A |
All |
1005997 |
3.91 % |
| Transition |
T>C |
All |
7276905 |
28.25 % |
| Transition |
C>T |
All |
1138025 |
4.42 % |
| Transversion |
A>C |
All |
672738 |
2.61 % |
| Transversion |
C>A |
All |
1284410 |
4.99 % |
| Transversion |
T>G |
All |
812455 |
3.15 % |
| Transversion |
G>T |
All |
1151876 |
4.47 % |
| Transversion |
A>T |
All |
700490 |
2.72 % |
| Transversion |
T>A |
All |
852178 |
3.31 % |
| Transversion |
C>G |
All |
775102 |
3.01 % |
| Transversion |
G>C |
All |
651497 |
2.53 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
674316 |
20.83 % |
| Transition |
G>A |
Passed |
416798 |
12.87 % |
| Transition |
T>C |
Passed |
675629 |
20.87 % |
| Transition |
C>T |
Passed |
436712 |
13.49 % |
| Transversion |
A>C |
Passed |
126696 |
3.91 % |
| Transversion |
C>A |
Passed |
140570 |
4.34 % |
| Transversion |
T>G |
Passed |
134784 |
4.16 % |
| Transversion |
G>T |
Passed |
139116 |
4.30 % |
| Transversion |
A>T |
Passed |
122689 |
3.79 % |
| Transversion |
T>A |
Passed |
122220 |
3.78 % |
| Transversion |
C>G |
Passed |
126704 |
3.91 % |
| Transversion |
G>C |
Passed |
121067 |
3.74 % |
| |
|
|
|
|
| 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 |
2.73 |
18860677 |
6900746 |
| Passed |
2.13 |
2203455 |
1033846 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |