/CEMT/variants/A75624_1_lane_gembs
BACK
SAMPLE A75624_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1176808757 |
1017893313 |
86.50 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1176808757 |
100% |
1158082202 |
98.41 % |
18726555 |
1.59 % |
| |
|
|
|
|
|
|
| Passed |
1020276261 |
86.70 % |
1014717141 |
87.62 % |
5559120 |
0.54 % |
| Filtered |
156532496 |
13.30 % |
143365061 |
12.38 % |
13167435 |
1.29 % |
| |
|
|
|
|
|
|
| q20 |
122487499 |
78.25 % |
121404768 |
84.68 % |
1082731 |
8.22 % |
| q20,qd2 |
14750478 |
9.42 % |
3686832 |
2.57 % |
11063646 |
84.02 % |
| q20,mq40 |
11615274 |
7.42 % |
11485588 |
8.01 % |
129686 |
0.98 % |
| mq40 |
2890073 |
1.85 % |
2623724 |
1.83 % |
266349 |
2.02 % |
| q20,qd2,mq40 |
2630802 |
1.68 % |
2469035 |
1.72 % |
161767 |
1.23 % |
| qd2 |
2105715 |
1.35 % |
1653331 |
1.15 % |
452384 |
3.44 % |
| qd2,mq40 |
51199 |
0.03 % |
41783 |
0.03 % |
9416 |
0.07 % |
| qd2,fs60,mq40 |
659 |
0.00 % |
0 |
0.00 % |
659 |
0.01 % |
| qd2,fs60 |
303 |
0.00 % |
0 |
0.00 % |
303 |
0.00 % |
| fs60,mq40 |
246 |
0.00 % |
0 |
0.00 % |
246 |
0.00 % |
| fs60 |
153 |
0.00 % |
0 |
0.00 % |
153 |
0.00 % |
| q20,qd2,fs60,mq40 |
55 |
0.00 % |
0 |
0.00 % |
55 |
0.00 % |
| q20,qd2,fs60 |
40 |
0.00 % |
0 |
0.00 % |
40 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
7543177 |
36.89 % |
| Transition |
G>A |
All |
947886 |
4.64 % |
| Transition |
T>C |
All |
7625626 |
37.30 % |
| Transition |
C>T |
All |
953654 |
4.66 % |
| Transversion |
A>C |
All |
371741 |
1.82 % |
| Transversion |
C>A |
All |
495863 |
2.43 % |
| Transversion |
T>G |
All |
376531 |
1.84 % |
| Transversion |
G>T |
All |
483154 |
2.36 % |
| Transversion |
A>T |
All |
496065 |
2.43 % |
| Transversion |
T>A |
All |
508247 |
2.49 % |
| Transversion |
C>G |
All |
323761 |
1.58 % |
| Transversion |
G>C |
All |
319924 |
1.56 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
948689 |
21.72 % |
| Transition |
G>A |
Passed |
601709 |
13.77 % |
| Transition |
T>C |
Passed |
850817 |
19.48 % |
| Transition |
C>T |
Passed |
598722 |
13.71 % |
| Transversion |
A>C |
Passed |
180675 |
4.14 % |
| Transversion |
C>A |
Passed |
182257 |
4.17 % |
| Transversion |
T>G |
Passed |
183833 |
4.21 % |
| Transversion |
G>T |
Passed |
172256 |
3.94 % |
| Transversion |
A>T |
Passed |
152513 |
3.49 % |
| Transversion |
T>A |
Passed |
156955 |
3.59 % |
| Transversion |
C>G |
Passed |
170781 |
3.91 % |
| Transversion |
G>C |
Passed |
169284 |
3.88 % |
| |
|
|
|
|
| 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 |
5.06 |
17070343 |
3375286 |
| Passed |
2.19 |
2999937 |
1368554 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |