/cemt/variants/A36010_3_lane_gembs
BACK
SAMPLE A36010_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1166269587 |
805803599 |
69.09 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1166269587 |
100% |
1148188248 |
98.45 % |
18081339 |
1.55 % |
| |
|
|
|
|
|
|
| Passed |
808054179 |
69.29 % |
803173680 |
69.95 % |
4880499 |
0.60 % |
| Filtered |
358215408 |
30.71 % |
345014568 |
30.05 % |
13200840 |
1.63 % |
| |
|
|
|
|
|
|
| q20 |
316510325 |
88.36 % |
313411570 |
90.84 % |
3098755 |
23.47 % |
| q20,qd2 |
19762665 |
5.52 % |
10535450 |
3.05 % |
9227215 |
69.90 % |
| q20,mq40 |
11738033 |
3.28 % |
11511815 |
3.34 % |
226218 |
1.71 % |
| qd2 |
4675082 |
1.31 % |
4467187 |
1.29 % |
207895 |
1.57 % |
| q20,qd2,mq40 |
3249430 |
0.91 % |
3007942 |
0.87 % |
241488 |
1.83 % |
| mq40 |
2199959 |
0.61 % |
2018086 |
0.58 % |
181873 |
1.38 % |
| qd2,mq40 |
73609 |
0.02 % |
62518 |
0.02 % |
11091 |
0.08 % |
| q20,qd2,fs60 |
1549 |
0.00 % |
0 |
0.00 % |
1549 |
0.01 % |
| fs60 |
1459 |
0.00 % |
0 |
0.00 % |
1459 |
0.01 % |
| qd2,fs60,mq40 |
1396 |
0.00 % |
0 |
0.00 % |
1396 |
0.01 % |
| qd2,fs60 |
1313 |
0.00 % |
0 |
0.00 % |
1313 |
0.01 % |
| fs60,mq40 |
401 |
0.00 % |
0 |
0.00 % |
401 |
0.00 % |
| q20,qd2,fs60,mq40 |
176 |
0.00 % |
0 |
0.00 % |
176 |
0.00 % |
| q20,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
5817445 |
28.97 % |
| Transition |
G>A |
All |
1612638 |
8.03 % |
| Transition |
T>C |
All |
5613403 |
27.95 % |
| Transition |
C>T |
All |
1612138 |
8.03 % |
| Transversion |
A>C |
All |
437191 |
2.18 % |
| Transversion |
C>A |
All |
943865 |
4.70 % |
| Transversion |
T>G |
All |
449832 |
2.24 % |
| Transversion |
G>T |
All |
941293 |
4.69 % |
| Transversion |
A>T |
All |
951503 |
4.74 % |
| Transversion |
T>A |
All |
964703 |
4.80 % |
| Transversion |
C>G |
All |
373733 |
1.86 % |
| Transversion |
G>C |
All |
364388 |
1.81 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
627200 |
17.57 % |
| Transition |
G>A |
Passed |
557680 |
15.62 % |
| Transition |
T>C |
Passed |
624036 |
17.48 % |
| Transition |
C>T |
Passed |
561191 |
15.72 % |
| Transversion |
A>C |
Passed |
150685 |
4.22 % |
| Transversion |
C>A |
Passed |
161886 |
4.54 % |
| Transversion |
T>G |
Passed |
151424 |
4.24 % |
| Transversion |
G>T |
Passed |
160027 |
4.48 % |
| Transversion |
A>T |
Passed |
146832 |
4.11 % |
| Transversion |
T>A |
Passed |
148013 |
4.15 % |
| Transversion |
C>G |
Passed |
140210 |
3.93 % |
| Transversion |
G>C |
Passed |
140216 |
3.93 % |
| |
|
|
|
|
| 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 |
2.70 |
14655624 |
5426508 |
| Passed |
1.98 |
2370107 |
1199293 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |