/EXTERNAL CREST/variants/K006475_1_lane_gembs
BACK
SAMPLE K006475_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1136544792 |
30733577 |
2.70 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1136544792 |
100% |
1065994361 |
93.79 % |
70550431 |
6.21 % |
| |
|
|
|
|
|
|
| Passed |
58113987 |
5.11 % |
29960407 |
2.81 % |
28153580 |
48.45 % |
| Filtered |
1078430805 |
94.89 % |
1036033954 |
97.19 % |
42396851 |
72.95 % |
| |
|
|
|
|
|
|
| q20 |
911977493 |
84.57 % |
891997334 |
86.10 % |
19980159 |
47.13 % |
| q20,qd2 |
85644659 |
7.94 % |
66510277 |
6.42 % |
19134382 |
45.13 % |
| q20,mq40 |
61516515 |
5.70 % |
60476289 |
5.84 % |
1040226 |
2.45 % |
| q20,qd2,mq40 |
17111440 |
1.59 % |
16481827 |
1.59 % |
629613 |
1.49 % |
| mq40 |
2172977 |
0.20 % |
562348 |
0.05 % |
1610629 |
3.80 % |
| qd2 |
4147 |
0.00 % |
3281 |
0.00 % |
866 |
0.00 % |
| qd2,mq40 |
3547 |
0.00 % |
2598 |
0.00 % |
949 |
0.00 % |
| fs60,mq40 |
20 |
0.00 % |
0 |
0.00 % |
20 |
0.00 % |
| fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
10758347 |
14.15 % |
| Transition |
G>A |
All |
4850547 |
6.38 % |
| Transition |
T>C |
All |
10359378 |
13.63 % |
| Transition |
C>T |
All |
3381857 |
4.45 % |
| Transversion |
A>C |
All |
2706043 |
3.56 % |
| Transversion |
C>A |
All |
7182205 |
9.45 % |
| Transversion |
T>G |
All |
4485688 |
5.90 % |
| Transversion |
G>T |
All |
7272431 |
9.57 % |
| Transversion |
A>T |
All |
9749240 |
12.82 % |
| Transversion |
T>A |
All |
9718944 |
12.78 % |
| Transversion |
C>G |
All |
3379617 |
4.45 % |
| Transversion |
G>C |
All |
2182145 |
2.87 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
142071 |
17.98 % |
| Transition |
G>A |
Passed |
52281 |
6.62 % |
| Transition |
T>C |
Passed |
133801 |
16.94 % |
| Transition |
C>T |
Passed |
22357 |
2.83 % |
| Transversion |
A>C |
Passed |
40829 |
5.17 % |
| Transversion |
C>A |
Passed |
63314 |
8.01 % |
| Transversion |
T>G |
Passed |
76918 |
9.74 % |
| Transversion |
G>T |
Passed |
37506 |
4.75 % |
| Transversion |
A>T |
Passed |
44426 |
5.62 % |
| Transversion |
T>A |
Passed |
82190 |
10.40 % |
| Transversion |
C>G |
Passed |
59081 |
7.48 % |
| Transversion |
G>C |
Passed |
35180 |
4.45 % |
| |
|
|
|
|
| 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 |
0.63 |
29350129 |
46676313 |
| Passed |
0.80 |
350510 |
439444 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |