/EXTERNAL BLUEPRINT/variants/K011964_K011965_K011966_K011967_K011968_K011969_K011970_7_lane_gembs
BACK
SAMPLE K011964_K011965_K011966_K011967_K011968_K011969_K011970_7_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
614573720 |
684961 |
0.11 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
614573720 |
100% |
608772393 |
99.06 % |
5801327 |
0.94 % |
| |
|
|
|
|
|
|
| Passed |
3881578 |
0.63 % |
577728 |
0.09 % |
3303850 |
85.12 % |
| Filtered |
610692142 |
99.37 % |
608194665 |
99.91 % |
2497477 |
64.34 % |
| |
|
|
|
|
|
|
| q20 |
488268563 |
79.95 % |
486436203 |
79.98 % |
1832360 |
73.37 % |
| q20,qd2 |
72641089 |
11.89 % |
72312810 |
11.89 % |
328279 |
13.14 % |
| q20,mq40 |
39034538 |
6.39 % |
38899087 |
6.40 % |
135451 |
5.42 % |
| q20,qd2,mq40 |
10526125 |
1.72 % |
10502264 |
1.73 % |
23861 |
0.96 % |
| mq40 |
221087 |
0.04 % |
43737 |
0.01 % |
177350 |
7.10 % |
| qd2,mq40 |
448 |
0.00 % |
356 |
0.00 % |
92 |
0.00 % |
| qd2 |
283 |
0.00 % |
208 |
0.00 % |
75 |
0.00 % |
| fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
2141152 |
20.67 % |
| Transition |
G>A |
All |
762122 |
7.36 % |
| Transition |
T>C |
All |
2936311 |
28.35 % |
| Transition |
C>T |
All |
400708 |
3.87 % |
| Transversion |
A>C |
All |
403361 |
3.89 % |
| Transversion |
C>A |
All |
638266 |
6.16 % |
| Transversion |
T>G |
All |
410435 |
3.96 % |
| Transversion |
G>T |
All |
596318 |
5.76 % |
| Transversion |
A>T |
All |
514229 |
4.96 % |
| Transversion |
T>A |
All |
694424 |
6.70 % |
| Transversion |
C>G |
All |
393143 |
3.80 % |
| Transversion |
G>C |
All |
466667 |
4.51 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
15143 |
14.26 % |
| Transition |
G>A |
Passed |
13398 |
12.61 % |
| Transition |
T>C |
Passed |
25180 |
23.71 % |
| Transition |
C>T |
Passed |
5911 |
5.57 % |
| Transversion |
A>C |
Passed |
5835 |
5.49 % |
| Transversion |
C>A |
Passed |
6060 |
5.71 % |
| Transversion |
T>G |
Passed |
5167 |
4.86 % |
| Transversion |
G>T |
Passed |
4250 |
4.00 % |
| Transversion |
A>T |
Passed |
3104 |
2.92 % |
| Transversion |
T>A |
Passed |
6783 |
6.39 % |
| Transversion |
C>G |
Passed |
6437 |
6.06 % |
| Transversion |
G>C |
Passed |
8941 |
8.42 % |
| |
|
|
|
|
| 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 |
1.52 |
6240293 |
4116843 |
| Passed |
1.28 |
59632 |
46577 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |