/EXTERNAL BLUEPRINT/variants/K006305_17_lane_gembs
BACK
SAMPLE K006305_17_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1112112779 |
586714297 |
52.76 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1112112779 |
100% |
1095724831 |
98.53 % |
16387948 |
1.47 % |
| |
|
|
|
|
|
|
| Passed |
588841986 |
52.95 % |
585346868 |
53.42 % |
3495118 |
0.59 % |
| Filtered |
523270793 |
47.05 % |
510377963 |
46.58 % |
12892830 |
2.19 % |
| |
|
|
|
|
|
|
| q20 |
453680625 |
86.70 % |
451544828 |
88.47 % |
2135797 |
16.57 % |
| q20,qd2 |
47008713 |
8.98 % |
36763459 |
7.20 % |
10245254 |
79.46 % |
| q20,mq40 |
12907581 |
2.47 % |
12808929 |
2.51 % |
98652 |
0.77 % |
| q20,qd2,mq40 |
3721297 |
0.71 % |
3583964 |
0.70 % |
137333 |
1.07 % |
| qd2 |
3127065 |
0.60 % |
3018226 |
0.59 % |
108839 |
0.84 % |
| mq40 |
2735257 |
0.52 % |
2589513 |
0.51 % |
145744 |
1.13 % |
| qd2,mq40 |
81417 |
0.02 % |
69044 |
0.01 % |
12373 |
0.10 % |
| q20,qd2,fs60 |
2188 |
0.00 % |
0 |
0.00 % |
2188 |
0.02 % |
| qd2,fs60,mq40 |
2100 |
0.00 % |
0 |
0.00 % |
2100 |
0.02 % |
| qd2,fs60 |
1682 |
0.00 % |
0 |
0.00 % |
1682 |
0.01 % |
| fs60 |
1474 |
0.00 % |
0 |
0.00 % |
1474 |
0.01 % |
| q20,qd2,fs60,mq40 |
718 |
0.00 % |
0 |
0.00 % |
718 |
0.01 % |
| fs60,mq40 |
669 |
0.00 % |
0 |
0.00 % |
669 |
0.01 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60 |
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 |
3650795 |
16.82 % |
| Transition |
G>A |
All |
5686766 |
26.20 % |
| Transition |
T>C |
All |
3324830 |
15.32 % |
| Transition |
C>T |
All |
5660672 |
26.08 % |
| Transversion |
A>C |
All |
238460 |
1.10 % |
| Transversion |
C>A |
All |
688279 |
3.17 % |
| Transversion |
T>G |
All |
278563 |
1.28 % |
| Transversion |
G>T |
All |
667021 |
3.07 % |
| Transversion |
A>T |
All |
533991 |
2.46 % |
| Transversion |
T>A |
All |
542503 |
2.50 % |
| Transversion |
C>G |
All |
223923 |
1.03 % |
| Transversion |
G>C |
All |
206233 |
0.95 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
388293 |
19.79 % |
| Transition |
G>A |
Passed |
324012 |
16.51 % |
| Transition |
T>C |
Passed |
384346 |
19.59 % |
| Transition |
C>T |
Passed |
323953 |
16.51 % |
| Transversion |
A>C |
Passed |
71119 |
3.62 % |
| Transversion |
C>A |
Passed |
67024 |
3.42 % |
| Transversion |
T>G |
Passed |
71175 |
3.63 % |
| Transversion |
G>T |
Passed |
66440 |
3.39 % |
| Transversion |
A>T |
Passed |
46560 |
2.37 % |
| Transversion |
T>A |
Passed |
46893 |
2.39 % |
| Transversion |
C>G |
Passed |
86033 |
4.38 % |
| Transversion |
G>C |
Passed |
86454 |
4.41 % |
| |
|
|
|
|
| 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 |
5.42 |
18323063 |
3378973 |
| Passed |
2.62 |
1420604 |
541698 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |