/EXTERNAL BLUEPRINT/variants/K011930_K011935_K011936_K011937_4_lane_gembs
BACK
SAMPLE K011930_K011935_K011936_K011937_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
612731820 |
255938 |
0.04 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
612731820 |
100% |
607217691 |
99.10 % |
5514129 |
0.90 % |
| |
|
|
|
|
|
|
| Passed |
3112612 |
0.51 % |
167310 |
0.03 % |
2945302 |
94.62 % |
| Filtered |
609619208 |
99.49 % |
607050381 |
99.97 % |
2568827 |
82.53 % |
| |
|
|
|
|
|
|
| q20 |
392804309 |
64.43 % |
390859408 |
64.39 % |
1944901 |
75.71 % |
| q20,qd2 |
160651015 |
26.35 % |
160371264 |
26.42 % |
279751 |
10.89 % |
| q20,mq40 |
35667908 |
5.85 % |
35528405 |
5.85 % |
139503 |
5.43 % |
| q20,qd2,mq40 |
20291457 |
3.33 % |
20266089 |
3.34 % |
25368 |
0.99 % |
| mq40 |
199154 |
0.03 % |
20038 |
0.00 % |
179116 |
6.97 % |
| qd2 |
4757 |
0.00 % |
4700 |
0.00 % |
57 |
0.00 % |
| qd2,mq40 |
577 |
0.00 % |
477 |
0.00 % |
100 |
0.00 % |
| qd2,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
2291498 |
22.66 % |
| Transition |
G>A |
All |
806869 |
7.98 % |
| Transition |
T>C |
All |
2890378 |
28.58 % |
| Transition |
C>T |
All |
398004 |
3.94 % |
| Transversion |
A>C |
All |
328554 |
3.25 % |
| Transversion |
C>A |
All |
623331 |
6.16 % |
| Transversion |
T>G |
All |
409811 |
4.05 % |
| Transversion |
G>T |
All |
565670 |
5.59 % |
| Transversion |
A>T |
All |
461025 |
4.56 % |
| Transversion |
T>A |
All |
627519 |
6.20 % |
| Transversion |
C>G |
All |
325924 |
3.22 % |
| Transversion |
G>C |
All |
384643 |
3.80 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
14618 |
16.74 % |
| Transition |
G>A |
Passed |
12033 |
13.78 % |
| Transition |
T>C |
Passed |
20486 |
23.45 % |
| Transition |
C>T |
Passed |
4127 |
4.72 % |
| Transversion |
A>C |
Passed |
3750 |
4.29 % |
| Transversion |
C>A |
Passed |
6505 |
7.45 % |
| Transversion |
T>G |
Passed |
4403 |
5.04 % |
| Transversion |
G>T |
Passed |
3390 |
3.88 % |
| Transversion |
A>T |
Passed |
1933 |
2.21 % |
| Transversion |
T>A |
Passed |
5282 |
6.05 % |
| Transversion |
C>G |
Passed |
4356 |
4.99 % |
| Transversion |
G>C |
Passed |
6461 |
7.40 % |
| |
|
|
|
|
| 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 |
1.71 |
6386749 |
3726477 |
| Passed |
1.42 |
51264 |
36080 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |