/cemt/variants/A56419_3_lane_gembs
BACK
SAMPLE A56419_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1166441347 |
745956196 |
63.95 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1166441347 |
100% |
1150636634 |
98.65 % |
15804713 |
1.35 % |
| |
|
|
|
|
|
|
| Passed |
749276030 |
64.24 % |
743702574 |
64.63 % |
5573456 |
0.74 % |
| Filtered |
417165317 |
35.76 % |
406934060 |
35.37 % |
10231257 |
1.37 % |
| |
|
|
|
|
|
|
| q20 |
380633120 |
91.24 % |
378021851 |
92.90 % |
2611269 |
25.52 % |
| q20,qd2 |
18747625 |
4.49 % |
11879179 |
2.92 % |
6868446 |
67.13 % |
| q20,mq40 |
10740854 |
2.57 % |
10614600 |
2.61 % |
126254 |
1.23 % |
| q20,qd2,mq40 |
2803063 |
0.67 % |
2654472 |
0.65 % |
148591 |
1.45 % |
| mq40 |
2335620 |
0.56 % |
2110700 |
0.52 % |
224920 |
2.20 % |
| qd2 |
1840898 |
0.44 % |
1602780 |
0.39 % |
238118 |
2.33 % |
| qd2,mq40 |
60532 |
0.01 % |
50478 |
0.01 % |
10054 |
0.10 % |
| qd2,fs60,mq40 |
1258 |
0.00 % |
0 |
0.00 % |
1258 |
0.01 % |
| qd2,fs60 |
804 |
0.00 % |
0 |
0.00 % |
804 |
0.01 % |
| fs60 |
595 |
0.00 % |
0 |
0.00 % |
595 |
0.01 % |
| fs60,mq40 |
424 |
0.00 % |
0 |
0.00 % |
424 |
0.00 % |
| q20,qd2,fs60 |
351 |
0.00 % |
0 |
0.00 % |
351 |
0.00 % |
| q20,qd2,fs60,mq40 |
171 |
0.00 % |
0 |
0.00 % |
171 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
6207463 |
35.02 % |
| Transition |
G>A |
All |
857935 |
4.84 % |
| Transition |
T>C |
All |
6233737 |
35.17 % |
| Transition |
C>T |
All |
870593 |
4.91 % |
| Transversion |
A>C |
All |
507313 |
2.86 % |
| Transversion |
C>A |
All |
460219 |
2.60 % |
| Transversion |
T>G |
All |
507928 |
2.87 % |
| Transversion |
G>T |
All |
455030 |
2.57 % |
| Transversion |
A>T |
All |
407726 |
2.30 % |
| Transversion |
T>A |
All |
413209 |
2.33 % |
| Transversion |
C>G |
All |
401912 |
2.27 % |
| Transversion |
G>C |
All |
402349 |
2.27 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
622222 |
19.71 % |
| Transition |
G>A |
Passed |
459612 |
14.56 % |
| Transition |
T>C |
Passed |
591305 |
18.73 % |
| Transition |
C>T |
Passed |
460995 |
14.60 % |
| Transversion |
A>C |
Passed |
132761 |
4.21 % |
| Transversion |
C>A |
Passed |
135004 |
4.28 % |
| Transversion |
T>G |
Passed |
133458 |
4.23 % |
| Transversion |
G>T |
Passed |
130841 |
4.14 % |
| Transversion |
A>T |
Passed |
120952 |
3.83 % |
| Transversion |
T>A |
Passed |
122448 |
3.88 % |
| Transversion |
C>G |
Passed |
123640 |
3.92 % |
| Transversion |
G>C |
Passed |
123781 |
3.92 % |
| |
|
|
|
|
| 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 |
3.99 |
14169728 |
3555686 |
| Passed |
2.09 |
2134134 |
1022885 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |