/EXTERNAL BLUEPRINT/variants/K011801_K011811_K011812_K011813_K011814_K011815_K011816_K011817_K011818_K011851_K011852_11_lane_gembs
BACK
SAMPLE K011801_K011811_K011812_K011813_K011814_K011815_K011816_K011817_K011818_K011851_K011852_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
896430324 |
7595663 |
0.85 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
896430324 |
100% |
878165765 |
97.96 % |
18264559 |
2.04 % |
| |
|
|
|
|
|
|
| Passed |
17456004 |
1.95 % |
6979755 |
0.79 % |
10476249 |
60.02 % |
| Filtered |
878974320 |
98.05 % |
871186010 |
99.21 % |
7788310 |
44.62 % |
| |
|
|
|
|
|
|
| q20 |
681087050 |
77.49 % |
675668916 |
77.56 % |
5418134 |
69.57 % |
| q20,qd2 |
130309634 |
14.83 % |
128868699 |
14.79 % |
1440935 |
18.50 % |
| q20,mq40 |
48566283 |
5.53 % |
48248515 |
5.54 % |
317768 |
4.08 % |
| q20,qd2,mq40 |
18332935 |
2.09 % |
18254706 |
2.10 % |
78229 |
1.00 % |
| mq40 |
669952 |
0.08 % |
137477 |
0.02 % |
532475 |
6.84 % |
| qd2 |
6760 |
0.00 % |
6379 |
0.00 % |
381 |
0.00 % |
| qd2,mq40 |
1656 |
0.00 % |
1318 |
0.00 % |
338 |
0.00 % |
| fs60,mq40 |
16 |
0.00 % |
0 |
0.00 % |
16 |
0.00 % |
| qd2,fs60 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
5147809 |
22.72 % |
| Transition |
G>A |
All |
1862677 |
8.22 % |
| Transition |
T>C |
All |
6730375 |
29.70 % |
| Transition |
C>T |
All |
889811 |
3.93 % |
| Transversion |
A>C |
All |
702147 |
3.10 % |
| Transversion |
C>A |
All |
1354674 |
5.98 % |
| Transversion |
T>G |
All |
841282 |
3.71 % |
| Transversion |
G>T |
All |
1222040 |
5.39 % |
| Transversion |
A>T |
All |
999537 |
4.41 % |
| Transversion |
T>A |
All |
1375851 |
6.07 % |
| Transversion |
C>G |
All |
694685 |
3.07 % |
| Transversion |
G>C |
All |
836541 |
3.69 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
100481 |
16.44 % |
| Transition |
G>A |
Passed |
78336 |
12.82 % |
| Transition |
T>C |
Passed |
176886 |
28.95 % |
| Transition |
C>T |
Passed |
37517 |
6.14 % |
| Transversion |
A>C |
Passed |
24329 |
3.98 % |
| Transversion |
C>A |
Passed |
33442 |
5.47 % |
| Transversion |
T>G |
Passed |
26517 |
4.34 % |
| Transversion |
G>T |
Passed |
22957 |
3.76 % |
| Transversion |
A>T |
Passed |
14964 |
2.45 % |
| Transversion |
T>A |
Passed |
31930 |
5.23 % |
| Transversion |
C>G |
Passed |
27256 |
4.46 % |
| Transversion |
G>C |
Passed |
36431 |
5.96 % |
| |
|
|
|
|
| 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 |
1.82 |
14630672 |
8026757 |
| Passed |
1.81 |
393220 |
217826 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |