/CEMT/variants/E00612_8_lane_gembs
BACK
SAMPLE E00612_8_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1238843990 |
668127042 |
53.93 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1238843990 |
100% |
1118624954 |
90.30 % |
120219036 |
9.70 % |
| |
|
|
|
|
|
|
| Passed |
697814931 |
56.33 % |
660107505 |
59.01 % |
37707426 |
5.40 % |
| Filtered |
541029059 |
43.67 % |
458517449 |
40.99 % |
82511610 |
11.82 % |
| |
|
|
|
|
|
|
| q20 |
427448336 |
79.01 % |
403296198 |
87.96 % |
24152138 |
29.27 % |
| q20,qd2 |
86815911 |
16.05 % |
30364003 |
6.62 % |
56451908 |
68.42 % |
| qd2 |
14599191 |
2.70 % |
13473463 |
2.94 % |
1125728 |
1.36 % |
| q20,mq40 |
8014804 |
1.48 % |
7773413 |
1.70 % |
241391 |
0.29 % |
| q20,qd2,mq40 |
3364559 |
0.62 % |
3166286 |
0.69 % |
198273 |
0.24 % |
| mq40 |
754530 |
0.14 % |
420317 |
0.09 % |
334213 |
0.41 % |
| qd2,mq40 |
31675 |
0.01 % |
23769 |
0.01 % |
7906 |
0.01 % |
| qd2,fs60 |
33 |
0.00 % |
0 |
0.00 % |
33 |
0.00 % |
| qd2,fs60,mq40 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| fs60,mq40 |
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 |
32460738 |
26.42 % |
| Transition |
G>A |
All |
7327906 |
5.96 % |
| Transition |
T>C |
All |
27122182 |
22.07 % |
| Transition |
C>T |
All |
7724914 |
6.29 % |
| Transversion |
A>C |
All |
4397184 |
3.58 % |
| Transversion |
C>A |
All |
6019734 |
4.90 % |
| Transversion |
T>G |
All |
4862558 |
3.96 % |
| Transversion |
G>T |
All |
5952888 |
4.84 % |
| Transversion |
A>T |
All |
10576851 |
8.61 % |
| Transversion |
T>A |
All |
10733532 |
8.73 % |
| Transversion |
C>G |
All |
2991848 |
2.43 % |
| Transversion |
G>C |
All |
2711381 |
2.21 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2524607 |
29.62 % |
| Transition |
G>A |
Passed |
632680 |
7.42 % |
| Transition |
T>C |
Passed |
1946221 |
22.84 % |
| Transition |
C>T |
Passed |
672798 |
7.89 % |
| Transversion |
A>C |
Passed |
424931 |
4.99 % |
| Transversion |
C>A |
Passed |
242227 |
2.84 % |
| Transversion |
T>G |
Passed |
465047 |
5.46 % |
| Transversion |
G>T |
Passed |
253172 |
2.97 % |
| Transversion |
A>T |
Passed |
329272 |
3.86 % |
| Transversion |
T>A |
Passed |
313882 |
3.68 % |
| Transversion |
C>G |
Passed |
372846 |
4.37 % |
| Transversion |
G>C |
Passed |
344872 |
4.05 % |
| |
|
|
|
|
| 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 |
1.55 |
74635740 |
48245976 |
| Passed |
2.10 |
5776306 |
2746249 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |