/cemt/variants/A59693_3_lane_gembs
BACK
SAMPLE A59693_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1158940340 |
1057437262 |
91.24 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1158940340 |
100% |
1146773215 |
98.95 % |
12167125 |
1.05 % |
| |
|
|
|
|
|
|
| Passed |
1058028821 |
91.29 % |
1054346742 |
91.94 % |
3682079 |
0.35 % |
| Filtered |
100911519 |
8.71 % |
92426473 |
8.06 % |
8485046 |
0.80 % |
| |
|
|
|
|
|
|
| q20 |
67179609 |
66.57 % |
66126281 |
71.54 % |
1053328 |
12.41 % |
| q20,qd2 |
11235389 |
11.13 % |
4921455 |
5.32 % |
6313934 |
74.41 % |
| q20,mq40 |
11087061 |
10.99 % |
10857396 |
11.75 % |
229665 |
2.71 % |
| qd2 |
5275254 |
5.23 % |
4920840 |
5.32 % |
354414 |
4.18 % |
| mq40 |
3033176 |
3.01 % |
2803853 |
3.03 % |
229323 |
2.70 % |
| q20,qd2,mq40 |
3028587 |
3.00 % |
2739636 |
2.96 % |
288951 |
3.41 % |
| qd2,mq40 |
68802 |
0.07 % |
57012 |
0.06 % |
11790 |
0.14 % |
| qd2,fs60,mq40 |
1108 |
0.00 % |
0 |
0.00 % |
1108 |
0.01 % |
| fs60 |
730 |
0.00 % |
0 |
0.00 % |
730 |
0.01 % |
| q20,qd2,fs60 |
688 |
0.00 % |
0 |
0.00 % |
688 |
0.01 % |
| qd2,fs60 |
539 |
0.00 % |
0 |
0.00 % |
539 |
0.01 % |
| fs60,mq40 |
432 |
0.00 % |
0 |
0.00 % |
432 |
0.01 % |
| q20,qd2,fs60,mq40 |
135 |
0.00 % |
0 |
0.00 % |
135 |
0.00 % |
| q20,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
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 |
3353151 |
24.06 % |
| Transition |
G>A |
All |
1108338 |
7.95 % |
| Transition |
T>C |
All |
3349423 |
24.04 % |
| Transition |
C>T |
All |
1107484 |
7.95 % |
| Transversion |
A>C |
All |
459075 |
3.29 % |
| Transversion |
C>A |
All |
816959 |
5.86 % |
| Transversion |
T>G |
All |
453533 |
3.25 % |
| Transversion |
G>T |
All |
838094 |
6.01 % |
| Transversion |
A>T |
All |
915278 |
6.57 % |
| Transversion |
T>A |
All |
887178 |
6.37 % |
| Transversion |
C>G |
All |
321106 |
2.30 % |
| Transversion |
G>C |
All |
324498 |
2.33 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
717751 |
16.58 % |
| Transition |
G>A |
Passed |
648919 |
14.99 % |
| Transition |
T>C |
Passed |
721791 |
16.68 % |
| Transition |
C>T |
Passed |
650147 |
15.02 % |
| Transversion |
A>C |
Passed |
211852 |
4.90 % |
| Transversion |
C>A |
Passed |
219920 |
5.08 % |
| Transversion |
T>G |
Passed |
209575 |
4.84 % |
| Transversion |
G>T |
Passed |
217488 |
5.03 % |
| Transversion |
A>T |
Passed |
194630 |
4.50 % |
| Transversion |
T>A |
Passed |
194560 |
4.50 % |
| Transversion |
C>G |
Passed |
169829 |
3.92 % |
| Transversion |
G>C |
Passed |
171289 |
3.96 % |
| |
|
|
|
|
| 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 |
1.78 |
8918396 |
5015721 |
| Passed |
1.72 |
2738608 |
1589143 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |