/EXTERNAL BLUEPRINT/variants/K006344_12_lane_gembs
BACK
SAMPLE K006344_12_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1135128014 |
725091007 |
63.88 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1135128014 |
100% |
1119495237 |
98.62 % |
15632777 |
1.38 % |
| |
|
|
|
|
|
|
| Passed |
726938403 |
64.04 % |
723531119 |
64.63 % |
3407284 |
0.47 % |
| Filtered |
408189611 |
35.96 % |
395964118 |
35.37 % |
12225493 |
1.68 % |
| |
|
|
|
|
|
|
| q20 |
346284952 |
84.83 % |
344718855 |
87.06 % |
1566097 |
12.81 % |
| q20,qd2 |
35676214 |
8.74 % |
25658732 |
6.48 % |
10017482 |
81.94 % |
| q20,mq40 |
13972444 |
3.42 % |
13855917 |
3.50 % |
116527 |
0.95 % |
| mq40 |
6589672 |
1.61 % |
6405035 |
1.62 % |
184637 |
1.51 % |
| q20,qd2,mq40 |
3120786 |
0.76 % |
2904086 |
0.73 % |
216700 |
1.77 % |
| qd2 |
2450085 |
0.60 % |
2345174 |
0.59 % |
104911 |
0.86 % |
| qd2,mq40 |
88525 |
0.02 % |
76319 |
0.02 % |
12206 |
0.10 % |
| q20,qd2,fs60 |
2355 |
0.00 % |
0 |
0.00 % |
2355 |
0.02 % |
| fs60 |
1530 |
0.00 % |
0 |
0.00 % |
1530 |
0.01 % |
| qd2,fs60,mq40 |
1130 |
0.00 % |
0 |
0.00 % |
1130 |
0.01 % |
| qd2,fs60 |
882 |
0.00 % |
0 |
0.00 % |
882 |
0.01 % |
| fs60,mq40 |
546 |
0.00 % |
0 |
0.00 % |
546 |
0.00 % |
| q20,qd2,fs60,mq40 |
486 |
0.00 % |
0 |
0.00 % |
486 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3470392 |
19.33 % |
| Transition |
G>A |
All |
4095383 |
22.81 % |
| Transition |
T>C |
All |
3332811 |
18.57 % |
| Transition |
C>T |
All |
4012419 |
22.35 % |
| Transversion |
A>C |
All |
227445 |
1.27 % |
| Transversion |
C>A |
All |
637594 |
3.55 % |
| Transversion |
T>G |
All |
239278 |
1.33 % |
| Transversion |
G>T |
All |
641355 |
3.57 % |
| Transversion |
A>T |
All |
460395 |
2.56 % |
| Transversion |
T>A |
All |
444325 |
2.48 % |
| Transversion |
C>G |
All |
198791 |
1.11 % |
| Transversion |
G>C |
All |
191474 |
1.07 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
419566 |
18.10 % |
| Transition |
G>A |
Passed |
396540 |
17.10 % |
| Transition |
T>C |
Passed |
418789 |
18.06 % |
| Transition |
C>T |
Passed |
398131 |
17.17 % |
| Transversion |
A>C |
Passed |
91155 |
3.93 % |
| Transversion |
C>A |
Passed |
86865 |
3.75 % |
| Transversion |
T>G |
Passed |
90655 |
3.91 % |
| Transversion |
G>T |
Passed |
87387 |
3.77 % |
| Transversion |
A>T |
Passed |
61252 |
2.64 % |
| Transversion |
T>A |
Passed |
61622 |
2.66 % |
| Transversion |
C>G |
Passed |
102687 |
4.43 % |
| Transversion |
G>C |
Passed |
103635 |
4.47 % |
| |
|
|
|
|
| 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 |
4.90 |
14911005 |
3040657 |
| Passed |
2.38 |
1633026 |
685258 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |