/EXTERNAL BLUEPRINT/variants/K012134_1_lane_gembs
BACK
SAMPLE K012134_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
529781361 |
149951 |
0.03 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
529781361 |
100% |
525864021 |
99.26 % |
3917340 |
0.74 % |
| |
|
|
|
|
|
|
| Passed |
2122139 |
0.40 % |
108175 |
0.02 % |
2013964 |
94.90 % |
| Filtered |
527659222 |
99.60 % |
525755846 |
99.98 % |
1903376 |
89.69 % |
| |
|
|
|
|
|
|
| q20 |
322785476 |
61.17 % |
321300001 |
61.11 % |
1485475 |
78.04 % |
| q20,qd2 |
155855501 |
29.54 % |
155687647 |
29.61 % |
167854 |
8.82 % |
| q20,mq40 |
29799704 |
5.65 % |
29691056 |
5.65 % |
108648 |
5.71 % |
| q20,qd2,mq40 |
19066902 |
3.61 % |
19050738 |
3.62 % |
16164 |
0.85 % |
| mq40 |
150866 |
0.03 % |
25737 |
0.00 % |
125129 |
6.57 % |
| qd2 |
528 |
0.00 % |
482 |
0.00 % |
46 |
0.00 % |
| qd2,mq40 |
230 |
0.00 % |
185 |
0.00 % |
45 |
0.00 % |
| fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,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 % |
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 |
1785954 |
22.52 % |
| Transition |
G>A |
All |
643882 |
8.12 % |
| Transition |
T>C |
All |
2329130 |
29.37 % |
| Transition |
C>T |
All |
322631 |
4.07 % |
| Transversion |
A>C |
All |
270836 |
3.42 % |
| Transversion |
C>A |
All |
463508 |
5.85 % |
| Transversion |
T>G |
All |
345390 |
4.36 % |
| Transversion |
G>T |
All |
418945 |
5.28 % |
| Transversion |
A>T |
All |
336649 |
4.25 % |
| Transversion |
T>A |
All |
462308 |
5.83 % |
| Transversion |
C>G |
All |
255521 |
3.22 % |
| Transversion |
G>C |
All |
294728 |
3.72 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
6331 |
15.39 % |
| Transition |
G>A |
Passed |
6212 |
15.10 % |
| Transition |
T>C |
Passed |
9972 |
24.24 % |
| Transition |
C>T |
Passed |
2340 |
5.69 % |
| Transversion |
A>C |
Passed |
1617 |
3.93 % |
| Transversion |
C>A |
Passed |
3004 |
7.30 % |
| Transversion |
T>G |
Passed |
2031 |
4.94 % |
| Transversion |
G>T |
Passed |
1459 |
3.55 % |
| Transversion |
A>T |
Passed |
830 |
2.02 % |
| Transversion |
T>A |
Passed |
2285 |
5.55 % |
| Transversion |
C>G |
Passed |
2071 |
5.03 % |
| Transversion |
G>C |
Passed |
2985 |
7.26 % |
| |
|
|
|
|
| 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 |
1.78 |
5081597 |
2847885 |
| Passed |
1.53 |
24855 |
16282 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |