/EXTERNAL BLUEPRINT/variants/K012037_K012072_K012073_K012074_K012075_K012076_K012077_K012078_K012114_K012115_10_lane_gembs
BACK
SAMPLE K012037_K012072_K012073_K012074_K012075_K012076_K012077_K012078_K012114_K012115_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
802623616 |
2122686 |
0.26 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
802623616 |
100% |
791297222 |
98.59 % |
11326394 |
1.41 % |
| |
|
|
|
|
|
|
| Passed |
8405290 |
1.05 % |
1887914 |
0.24 % |
6517376 |
77.54 % |
| Filtered |
794218326 |
98.95 % |
789409308 |
99.76 % |
4809018 |
57.21 % |
| |
|
|
|
|
|
|
| q20 |
614182579 |
77.33 % |
610695627 |
77.36 % |
3486952 |
72.51 % |
| q20,qd2 |
110859514 |
13.96 % |
110145228 |
13.95 % |
714286 |
14.85 % |
| q20,mq40 |
50179075 |
6.32 % |
49952539 |
6.33 % |
226536 |
4.71 % |
| q20,qd2,mq40 |
18597481 |
2.34 % |
18550185 |
2.35 % |
47296 |
0.98 % |
| mq40 |
394026 |
0.05 % |
60510 |
0.01 % |
333516 |
6.94 % |
| qd2 |
4410 |
0.00 % |
4256 |
0.00 % |
154 |
0.00 % |
| qd2,mq40 |
1218 |
0.00 % |
963 |
0.00 % |
255 |
0.01 % |
| fs60,mq40 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60 |
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 % |
| 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 |
3574659 |
22.45 % |
| Transition |
G>A |
All |
1256197 |
7.89 % |
| Transition |
T>C |
All |
4436412 |
27.86 % |
| Transition |
C>T |
All |
616911 |
3.87 % |
| Transversion |
A>C |
All |
565759 |
3.55 % |
| Transversion |
C>A |
All |
966320 |
6.07 % |
| Transversion |
T>G |
All |
665920 |
4.18 % |
| Transversion |
G>T |
All |
868902 |
5.46 % |
| Transversion |
A>T |
All |
761787 |
4.78 % |
| Transversion |
T>A |
All |
1054739 |
6.62 % |
| Transversion |
C>G |
All |
538125 |
3.38 % |
| Transversion |
G>C |
All |
620250 |
3.89 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
39024 |
16.75 % |
| Transition |
G>A |
Passed |
30161 |
12.94 % |
| Transition |
T>C |
Passed |
54885 |
23.55 % |
| Transition |
C>T |
Passed |
15054 |
6.46 % |
| Transversion |
A>C |
Passed |
10277 |
4.41 % |
| Transversion |
C>A |
Passed |
14544 |
6.24 % |
| Transversion |
T>G |
Passed |
11639 |
4.99 % |
| Transversion |
G>T |
Passed |
9971 |
4.28 % |
| Transversion |
A>T |
Passed |
6099 |
2.62 % |
| Transversion |
T>A |
Passed |
13079 |
5.61 % |
| Transversion |
C>G |
Passed |
12806 |
5.50 % |
| Transversion |
G>C |
Passed |
15502 |
6.65 % |
| |
|
|
|
|
| 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 |
9884179 |
6041802 |
| Passed |
1.48 |
139124 |
93917 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |