/cemt/variants/A77953_1_lane_gembs
BACK
SAMPLE A77953_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170868929 |
1001804763 |
85.56 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170868929 |
100% |
1150216132 |
98.24 % |
20652797 |
1.76 % |
| |
|
|
|
|
|
|
| Passed |
1004554676 |
85.80 % |
998653077 |
86.82 % |
5901599 |
0.59 % |
| Filtered |
166314253 |
14.20 % |
151563055 |
13.18 % |
14751198 |
1.47 % |
| |
|
|
|
|
|
|
| q20 |
129932542 |
78.12 % |
128878399 |
85.03 % |
1054143 |
7.15 % |
| q20,qd2 |
17573714 |
10.57 % |
4921511 |
3.25 % |
12652203 |
85.77 % |
| q20,mq40 |
10908095 |
6.56 % |
10789335 |
7.12 % |
118760 |
0.81 % |
| q20,qd2,mq40 |
2713158 |
1.63 % |
2552874 |
1.68 % |
160284 |
1.09 % |
| qd2 |
2663205 |
1.60 % |
2172621 |
1.43 % |
490584 |
3.33 % |
| mq40 |
2475675 |
1.49 % |
2211074 |
1.46 % |
264601 |
1.79 % |
| qd2,mq40 |
46625 |
0.03 % |
37241 |
0.02 % |
9384 |
0.06 % |
| qd2,fs60,mq40 |
514 |
0.00 % |
0 |
0.00 % |
514 |
0.00 % |
| fs60,mq40 |
279 |
0.00 % |
0 |
0.00 % |
279 |
0.00 % |
| qd2,fs60 |
231 |
0.00 % |
0 |
0.00 % |
231 |
0.00 % |
| fs60 |
131 |
0.00 % |
0 |
0.00 % |
131 |
0.00 % |
| q20,qd2,fs60,mq40 |
54 |
0.00 % |
0 |
0.00 % |
54 |
0.00 % |
| q20,qd2,fs60 |
29 |
0.00 % |
0 |
0.00 % |
29 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
8095955 |
36.07 % |
| Transition |
G>A |
All |
970875 |
4.33 % |
| Transition |
T>C |
All |
8088414 |
36.04 % |
| Transition |
C>T |
All |
978877 |
4.36 % |
| Transversion |
A>C |
All |
334711 |
1.49 % |
| Transversion |
C>A |
All |
1032730 |
4.60 % |
| Transversion |
T>G |
All |
335710 |
1.50 % |
| Transversion |
G>T |
All |
864357 |
3.85 % |
| Transversion |
A>T |
All |
566722 |
2.52 % |
| Transversion |
T>A |
All |
580106 |
2.58 % |
| Transversion |
C>G |
All |
301415 |
1.34 % |
| Transversion |
G>C |
All |
295430 |
1.32 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
844691 |
19.40 % |
| Transition |
G>A |
Passed |
562836 |
12.93 % |
| Transition |
T>C |
Passed |
810115 |
18.61 % |
| Transition |
C>T |
Passed |
560955 |
12.89 % |
| Transversion |
A>C |
Passed |
166101 |
3.82 % |
| Transversion |
C>A |
Passed |
339697 |
7.80 % |
| Transversion |
T>G |
Passed |
167749 |
3.85 % |
| Transversion |
G>T |
Passed |
272373 |
6.26 % |
| Transversion |
A>T |
Passed |
153398 |
3.52 % |
| Transversion |
T>A |
Passed |
158837 |
3.65 % |
| Transversion |
C>G |
Passed |
158869 |
3.65 % |
| Transversion |
G>C |
Passed |
157556 |
3.62 % |
| |
|
|
|
|
| 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 |
4.21 |
18134121 |
4311181 |
| Passed |
1.76 |
2778597 |
1574580 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |