/EXTERNAL CREST/variants/K006462_1_lane_gembs
BACK
SAMPLE K006462_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1227852453 |
602993045 |
49.11 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1227852453 |
100% |
1103891535 |
89.90 % |
123960918 |
10.10 % |
| |
|
|
|
|
|
|
| Passed |
623707983 |
50.80 % |
595547095 |
53.95 % |
28160888 |
4.52 % |
| Filtered |
604144470 |
49.20 % |
508344440 |
46.05 % |
95800030 |
15.36 % |
| |
|
|
|
|
|
|
| q20 |
432665900 |
71.62 % |
406740625 |
80.01 % |
25925275 |
27.06 % |
| q20,qd2 |
93953655 |
15.55 % |
30826198 |
6.06 % |
63127457 |
65.90 % |
| q20,mq40 |
45001694 |
7.45 % |
43202198 |
8.50 % |
1799496 |
1.88 % |
| mq40 |
19089021 |
3.16 % |
17054363 |
3.35 % |
2034658 |
2.12 % |
| q20,qd2,mq40 |
7744674 |
1.28 % |
5385564 |
1.06 % |
2359110 |
2.46 % |
| qd2 |
5612565 |
0.93 % |
5073490 |
1.00 % |
539075 |
0.56 % |
| qd2,mq40 |
76309 |
0.01 % |
62002 |
0.01 % |
14307 |
0.01 % |
| fs60 |
337 |
0.00 % |
0 |
0.00 % |
337 |
0.00 % |
| fs60,mq40 |
274 |
0.00 % |
0 |
0.00 % |
274 |
0.00 % |
| q20,qd2,fs60 |
23 |
0.00 % |
0 |
0.00 % |
23 |
0.00 % |
| q20,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
28100617 |
22.28 % |
| Transition |
G>A |
All |
10904401 |
8.65 % |
| Transition |
T>C |
All |
32641840 |
25.88 % |
| Transition |
C>T |
All |
6777113 |
5.37 % |
| Transversion |
A>C |
All |
3154446 |
2.50 % |
| Transversion |
C>A |
All |
6913108 |
5.48 % |
| Transversion |
T>G |
All |
5290025 |
4.19 % |
| Transversion |
G>T |
All |
6371636 |
5.05 % |
| Transversion |
A>T |
All |
9544329 |
7.57 % |
| Transversion |
T>A |
All |
10596938 |
8.40 % |
| Transversion |
C>G |
All |
3469439 |
2.75 % |
| Transversion |
G>C |
All |
2359296 |
1.87 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1577772 |
19.89 % |
| Transition |
G>A |
Passed |
750696 |
9.46 % |
| Transition |
T>C |
Passed |
2189775 |
27.60 % |
| Transition |
C>T |
Passed |
411831 |
5.19 % |
| Transversion |
A>C |
Passed |
286090 |
3.61 % |
| Transversion |
C>A |
Passed |
432525 |
5.45 % |
| Transversion |
T>G |
Passed |
543511 |
6.85 % |
| Transversion |
G>T |
Passed |
200094 |
2.52 % |
| Transversion |
A>T |
Passed |
228991 |
2.89 % |
| Transversion |
T>A |
Passed |
637981 |
8.04 % |
| Transversion |
C>G |
Passed |
405576 |
5.11 % |
| Transversion |
G>C |
Passed |
268438 |
3.38 % |
| |
|
|
|
|
| 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 |
1.64 |
78423971 |
47699217 |
| Passed |
1.64 |
4930074 |
3003206 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |