/EXTERNAL BLUEPRINT/variants/K010441_K010442_K010443_K010444_K010445_K010446_K010447_K010448_K010449_K010450_10_lane_gembs
BACK
SAMPLE K010441_K010442_K010443_K010444_K010445_K010446_K010447_K010448_K010449_K010450_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
782741167 |
1838452 |
0.23 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
782741167 |
100% |
771552369 |
98.57 % |
11188798 |
1.43 % |
| |
|
|
|
|
|
|
| Passed |
6883715 |
0.88 % |
1553340 |
0.20 % |
5330375 |
77.43 % |
| Filtered |
775857452 |
99.12 % |
769999029 |
99.80 % |
5858423 |
85.11 % |
| |
|
|
|
|
|
|
| q20 |
546443455 |
70.43 % |
542101221 |
70.40 % |
4342234 |
74.12 % |
| q20,qd2 |
152612725 |
19.67 % |
151840598 |
19.72 % |
772127 |
13.18 % |
| q20,mq40 |
51781606 |
6.67 % |
51444598 |
6.68 % |
337008 |
5.75 % |
| q20,qd2,mq40 |
24603550 |
3.17 % |
24536606 |
3.19 % |
66944 |
1.14 % |
| mq40 |
410258 |
0.05 % |
70539 |
0.01 % |
339719 |
5.80 % |
| qd2 |
4600 |
0.00 % |
4453 |
0.00 % |
147 |
0.00 % |
| qd2,mq40 |
1234 |
0.00 % |
1014 |
0.00 % |
220 |
0.00 % |
| fs60,mq40 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| qd2,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 % |
| 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 |
3637121 |
22.70 % |
| Transition |
G>A |
All |
1275055 |
7.96 % |
| Transition |
T>C |
All |
4421497 |
27.60 % |
| Transition |
C>T |
All |
597374 |
3.73 % |
| Transversion |
A>C |
All |
554155 |
3.46 % |
| Transversion |
C>A |
All |
1039275 |
6.49 % |
| Transversion |
T>G |
All |
680759 |
4.25 % |
| Transversion |
G>T |
All |
920530 |
5.75 % |
| Transversion |
A>T |
All |
740151 |
4.62 % |
| Transversion |
T>A |
All |
1027175 |
6.41 % |
| Transversion |
C>G |
All |
522911 |
3.26 % |
| Transversion |
G>C |
All |
604720 |
3.77 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
52488 |
18.59 % |
| Transition |
G>A |
Passed |
39494 |
13.98 % |
| Transition |
T>C |
Passed |
70886 |
25.10 % |
| Transition |
C>T |
Passed |
13121 |
4.65 % |
| Transversion |
A>C |
Passed |
11179 |
3.96 % |
| Transversion |
C>A |
Passed |
19162 |
6.79 % |
| Transversion |
T>G |
Passed |
12963 |
4.59 % |
| Transversion |
G>T |
Passed |
9758 |
3.46 % |
| Transversion |
A>T |
Passed |
5564 |
1.97 % |
| Transversion |
T>A |
Passed |
16615 |
5.88 % |
| Transversion |
C>G |
Passed |
12905 |
4.57 % |
| Transversion |
G>C |
Passed |
18281 |
6.47 % |
| |
|
|
|
|
| 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 |
1.63 |
9931047 |
6089676 |
| Passed |
1.65 |
175989 |
106427 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |