/EXTERNAL BLUEPRINT/variants/K006396_K006409_19_lane_gembs
BACK
SAMPLE K006396_K006409_19_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1151991422 |
1018446892 |
88.41 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1151991422 |
100% |
1140818729 |
99.03 % |
11172693 |
0.97 % |
| |
|
|
|
|
|
|
| Passed |
1019641022 |
88.51 % |
1016162773 |
89.07 % |
3478249 |
0.34 % |
| Filtered |
132350400 |
11.49 % |
124655956 |
10.93 % |
7694444 |
0.75 % |
| |
|
|
|
|
|
|
| q20 |
93006857 |
70.27 % |
92098335 |
73.88 % |
908522 |
11.81 % |
| q20,mq40 |
11434547 |
8.64 % |
11334346 |
9.09 % |
100201 |
1.30 % |
| q20,qd2 |
9327158 |
7.05 % |
3221135 |
2.58 % |
6106023 |
79.36 % |
| qd2 |
8500332 |
6.42 % |
8337309 |
6.69 % |
163023 |
2.12 % |
| mq40 |
7197735 |
5.44 % |
6994077 |
5.61 % |
203658 |
2.65 % |
| q20,qd2,mq40 |
2760125 |
2.09 % |
2577630 |
2.07 % |
182495 |
2.37 % |
| qd2,mq40 |
108681 |
0.08 % |
93124 |
0.07 % |
15557 |
0.20 % |
| fs60 |
4259 |
0.00 % |
0 |
0.00 % |
4259 |
0.06 % |
| qd2,fs60 |
3537 |
0.00 % |
0 |
0.00 % |
3537 |
0.05 % |
| q20,qd2,fs60 |
3416 |
0.00 % |
0 |
0.00 % |
3416 |
0.04 % |
| qd2,fs60,mq40 |
2490 |
0.00 % |
0 |
0.00 % |
2490 |
0.03 % |
| fs60,mq40 |
893 |
0.00 % |
0 |
0.00 % |
893 |
0.01 % |
| q20,qd2,fs60,mq40 |
361 |
0.00 % |
0 |
0.00 % |
361 |
0.00 % |
| q20,fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
4214943 |
32.43 % |
| Transition |
G>A |
All |
1068897 |
8.22 % |
| Transition |
T>C |
All |
4185596 |
32.20 % |
| Transition |
C>T |
All |
1076508 |
8.28 % |
| Transversion |
A>C |
All |
214018 |
1.65 % |
| Transversion |
C>A |
All |
455724 |
3.51 % |
| Transversion |
T>G |
All |
217427 |
1.67 % |
| Transversion |
G>T |
All |
448842 |
3.45 % |
| Transversion |
A>T |
All |
360841 |
2.78 % |
| Transversion |
T>A |
All |
355535 |
2.74 % |
| Transversion |
C>G |
All |
201241 |
1.55 % |
| Transversion |
G>C |
All |
198792 |
1.53 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
595351 |
17.38 % |
| Transition |
G>A |
Passed |
557476 |
16.28 % |
| Transition |
T>C |
Passed |
597660 |
17.45 % |
| Transition |
C>T |
Passed |
558475 |
16.31 % |
| Transversion |
A>C |
Passed |
145616 |
4.25 % |
| Transversion |
C>A |
Passed |
144281 |
4.21 % |
| Transversion |
T>G |
Passed |
146719 |
4.28 % |
| Transversion |
G>T |
Passed |
144402 |
4.22 % |
| Transversion |
A>T |
Passed |
122931 |
3.59 % |
| Transversion |
T>A |
Passed |
123267 |
3.60 % |
| Transversion |
C>G |
Passed |
144320 |
4.21 % |
| Transversion |
G>C |
Passed |
144052 |
4.21 % |
| |
|
|
|
|
| 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 |
4.30 |
10545944 |
2452420 |
| Passed |
2.07 |
2308962 |
1115588 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |