/cemt/variants/A36013_3_lane_gembs
BACK
SAMPLE A36013_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156881454 |
715786762 |
61.87 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156881454 |
100% |
1137544912 |
98.33 % |
19336542 |
1.67 % |
| |
|
|
|
|
|
|
| Passed |
718514323 |
62.11 % |
713632726 |
62.73 % |
4881597 |
0.68 % |
| Filtered |
438367131 |
37.89 % |
423912186 |
37.27 % |
14454945 |
2.01 % |
| |
|
|
|
|
|
|
| q20 |
392096460 |
89.44 % |
388371127 |
91.62 % |
3725333 |
25.77 % |
| q20,qd2 |
24986268 |
5.70 % |
15000201 |
3.54 % |
9986067 |
69.08 % |
| q20,mq40 |
10699166 |
2.44 % |
10502984 |
2.48 % |
196182 |
1.36 % |
| qd2 |
5533316 |
1.26 % |
5350654 |
1.26 % |
182662 |
1.26 % |
| q20,qd2,mq40 |
3361628 |
0.77 % |
3160144 |
0.75 % |
201484 |
1.39 % |
| mq40 |
1628309 |
0.37 % |
1480478 |
0.35 % |
147831 |
1.02 % |
| qd2,mq40 |
54907 |
0.01 % |
46598 |
0.01 % |
8309 |
0.06 % |
| fs60 |
2120 |
0.00 % |
0 |
0.00 % |
2120 |
0.01 % |
| q20,qd2,fs60 |
2006 |
0.00 % |
0 |
0.00 % |
2006 |
0.01 % |
| qd2,fs60 |
1294 |
0.00 % |
0 |
0.00 % |
1294 |
0.01 % |
| qd2,fs60,mq40 |
1144 |
0.00 % |
0 |
0.00 % |
1144 |
0.01 % |
| fs60,mq40 |
326 |
0.00 % |
0 |
0.00 % |
326 |
0.00 % |
| q20,qd2,fs60,mq40 |
170 |
0.00 % |
0 |
0.00 % |
170 |
0.00 % |
| q20,fs60 |
15 |
0.00 % |
0 |
0.00 % |
15 |
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 |
5708807 |
26.50 % |
| Transition |
G>A |
All |
1868004 |
8.67 % |
| Transition |
T>C |
All |
5634094 |
26.15 % |
| Transition |
C>T |
All |
1876792 |
8.71 % |
| Transversion |
A>C |
All |
441729 |
2.05 % |
| Transversion |
C>A |
All |
1349338 |
6.26 % |
| Transversion |
T>G |
All |
446615 |
2.07 % |
| Transversion |
G>T |
All |
1352371 |
6.28 % |
| Transversion |
A>T |
All |
1067661 |
4.96 % |
| Transversion |
T>A |
All |
1067218 |
4.95 % |
| Transversion |
C>G |
All |
366964 |
1.70 % |
| Transversion |
G>C |
All |
364411 |
1.69 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
529818 |
17.47 % |
| Transition |
G>A |
Passed |
479445 |
15.81 % |
| Transition |
T>C |
Passed |
531490 |
17.52 % |
| Transition |
C>T |
Passed |
479466 |
15.81 % |
| Transversion |
A>C |
Passed |
124662 |
4.11 % |
| Transversion |
C>A |
Passed |
138890 |
4.58 % |
| Transversion |
T>G |
Passed |
124910 |
4.12 % |
| Transversion |
G>T |
Passed |
137617 |
4.54 % |
| Transversion |
A>T |
Passed |
125617 |
4.14 % |
| Transversion |
T>A |
Passed |
127348 |
4.20 % |
| Transversion |
C>G |
Passed |
117009 |
3.86 % |
| Transversion |
G>C |
Passed |
117067 |
3.86 % |
| |
|
|
|
|
| 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 |
2.34 |
15087697 |
6456307 |
| Passed |
1.99 |
2020219 |
1013120 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |