/CEMT/variants/E00609_8_lane_gembs
BACK
SAMPLE E00609_8_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1239424215 |
651358716 |
52.55 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1239424215 |
100% |
1116914412 |
90.12 % |
122509803 |
9.88 % |
| |
|
|
|
|
|
|
| Passed |
681956311 |
55.02 % |
643382514 |
57.60 % |
38573797 |
5.66 % |
| Filtered |
557467904 |
44.98 % |
473531898 |
42.40 % |
83936006 |
12.31 % |
| |
|
|
|
|
|
|
| q20 |
442368632 |
79.35 % |
416639218 |
87.99 % |
25729414 |
30.65 % |
| q20,qd2 |
88123660 |
15.81 % |
31796947 |
6.71 % |
56326713 |
67.11 % |
| qd2 |
14661316 |
2.63 % |
13575983 |
2.87 % |
1085333 |
1.29 % |
| q20,mq40 |
8088299 |
1.45 % |
7840045 |
1.66 % |
248254 |
0.30 % |
| q20,qd2,mq40 |
3418866 |
0.61 % |
3220203 |
0.68 % |
198663 |
0.24 % |
| mq40 |
772991 |
0.14 % |
433706 |
0.09 % |
339285 |
0.40 % |
| qd2,mq40 |
34081 |
0.01 % |
25796 |
0.01 % |
8285 |
0.01 % |
| qd2,fs60 |
37 |
0.00 % |
0 |
0.00 % |
37 |
0.00 % |
| qd2,fs60,mq40 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 % |
| q20,qd2,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 |
32934903 |
26.27 % |
| Transition |
G>A |
All |
7269745 |
5.80 % |
| Transition |
T>C |
All |
27269695 |
21.75 % |
| Transition |
C>T |
All |
7669893 |
6.12 % |
| Transversion |
A>C |
All |
4553873 |
3.63 % |
| Transversion |
C>A |
All |
6256060 |
4.99 % |
| Transversion |
T>G |
All |
5089463 |
4.06 % |
| Transversion |
G>T |
All |
6201639 |
4.95 % |
| Transversion |
A>T |
All |
10996214 |
8.77 % |
| Transversion |
T>A |
All |
11120047 |
8.87 % |
| Transversion |
C>G |
All |
3159140 |
2.52 % |
| Transversion |
G>C |
All |
2832877 |
2.26 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2517885 |
29.72 % |
| Transition |
G>A |
Passed |
616581 |
7.28 % |
| Transition |
T>C |
Passed |
1922449 |
22.69 % |
| Transition |
C>T |
Passed |
656313 |
7.75 % |
| Transversion |
A>C |
Passed |
428037 |
5.05 % |
| Transversion |
C>A |
Passed |
238830 |
2.82 % |
| Transversion |
T>G |
Passed |
471768 |
5.57 % |
| Transversion |
G>T |
Passed |
252558 |
2.98 % |
| Transversion |
A>T |
Passed |
326203 |
3.85 % |
| Transversion |
T>A |
Passed |
310701 |
3.67 % |
| Transversion |
C>G |
Passed |
381212 |
4.50 % |
| Transversion |
G>C |
Passed |
349349 |
4.12 % |
| |
|
|
|
|
| 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 |
1.50 |
75144236 |
50209313 |
| Passed |
2.07 |
5713228 |
2758658 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |