/EXTERNAL CREST/variants/K006447_1_lane_gembs
BACK
SAMPLE K006447_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1190417637 |
587287643 |
49.33 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1190417637 |
100% |
1109182929 |
93.18 % |
81234708 |
6.82 % |
| |
|
|
|
|
|
|
| Passed |
606547483 |
50.95 % |
582707564 |
52.53 % |
23839919 |
3.93 % |
| Filtered |
583870154 |
49.05 % |
526475365 |
47.47 % |
57394789 |
9.46 % |
| |
|
|
|
|
|
|
| q20 |
481883964 |
82.53 % |
462447559 |
87.84 % |
19436405 |
33.86 % |
| q20,qd2 |
66623661 |
11.41 % |
31004783 |
5.89 % |
35618878 |
62.06 % |
| q20,mq40 |
16270969 |
2.79 % |
15752839 |
2.99 % |
518130 |
0.90 % |
| qd2 |
10274249 |
1.76 % |
9659390 |
1.83 % |
614859 |
1.07 % |
| q20,qd2,mq40 |
6002031 |
1.03 % |
5501701 |
1.05 % |
500330 |
0.87 % |
| mq40 |
2759014 |
0.47 % |
2067172 |
0.39 % |
691842 |
1.21 % |
| qd2,mq40 |
53457 |
0.01 % |
41921 |
0.01 % |
11536 |
0.02 % |
| q20,qd2,fs60 |
1700 |
0.00 % |
0 |
0.00 % |
1700 |
0.00 % |
| fs60 |
488 |
0.00 % |
0 |
0.00 % |
488 |
0.00 % |
| qd2,fs60,mq40 |
190 |
0.00 % |
0 |
0.00 % |
190 |
0.00 % |
| qd2,fs60 |
171 |
0.00 % |
0 |
0.00 % |
171 |
0.00 % |
| fs60,mq40 |
162 |
0.00 % |
0 |
0.00 % |
162 |
0.00 % |
| q20,qd2,fs60,mq40 |
88 |
0.00 % |
0 |
0.00 % |
88 |
0.00 % |
| q20,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
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 |
20282641 |
23.96 % |
| Transition |
G>A |
All |
5915081 |
6.99 % |
| Transition |
T>C |
All |
20160920 |
23.82 % |
| Transition |
C>T |
All |
4979069 |
5.88 % |
| Transversion |
A>C |
All |
2705021 |
3.20 % |
| Transversion |
C>A |
All |
4382932 |
5.18 % |
| Transversion |
T>G |
All |
3562313 |
4.21 % |
| Transversion |
G>T |
All |
4210276 |
4.97 % |
| Transversion |
A>T |
All |
7044207 |
8.32 % |
| Transversion |
T>A |
All |
7480221 |
8.84 % |
| Transversion |
C>G |
All |
2141225 |
2.53 % |
| Transversion |
G>C |
All |
1780522 |
2.10 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1111317 |
21.66 % |
| Transition |
G>A |
Passed |
510579 |
9.95 % |
| Transition |
T>C |
Passed |
1340581 |
26.13 % |
| Transition |
C>T |
Passed |
462287 |
9.01 % |
| Transversion |
A>C |
Passed |
235755 |
4.60 % |
| Transversion |
C>A |
Passed |
195556 |
3.81 % |
| Transversion |
T>G |
Passed |
285850 |
5.57 % |
| Transversion |
G>T |
Passed |
161845 |
3.15 % |
| Transversion |
A>T |
Passed |
170048 |
3.31 % |
| Transversion |
T>A |
Passed |
237687 |
4.63 % |
| Transversion |
C>G |
Passed |
225225 |
4.39 % |
| Transversion |
G>C |
Passed |
193712 |
3.78 % |
| |
|
|
|
|
| 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 |
1.54 |
51337711 |
33306717 |
| Passed |
2.01 |
3424764 |
1705678 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |