/EXTERNAL McGill EMC/variants/K006193_1_lane_gembs
BACK
SAMPLE K006193_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1138521644 |
432925510 |
38.03 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1138521644 |
100% |
1126506476 |
98.94 % |
12015168 |
1.06 % |
| |
|
|
|
|
|
|
| Passed |
435467809 |
38.25 % |
431241246 |
38.28 % |
4226563 |
0.97 % |
| Filtered |
703053835 |
61.75 % |
695265230 |
61.72 % |
7788605 |
1.79 % |
| |
|
|
|
|
|
|
| q20 |
664459604 |
94.51 % |
662134349 |
95.23 % |
2325255 |
29.85 % |
| q20,qd2 |
20504993 |
2.92 % |
15360920 |
2.21 % |
5144073 |
66.05 % |
| q20,mq40 |
12532564 |
1.78 % |
12447742 |
1.79 % |
84822 |
1.09 % |
| q20,qd2,mq40 |
3996504 |
0.57 % |
3916811 |
0.56 % |
79693 |
1.02 % |
| qd2 |
870930 |
0.12 % |
834728 |
0.12 % |
36202 |
0.46 % |
| mq40 |
664330 |
0.09 % |
551252 |
0.08 % |
113078 |
1.45 % |
| qd2,mq40 |
24292 |
0.00 % |
19428 |
0.00 % |
4864 |
0.06 % |
| qd2,fs60,mq40 |
274 |
0.00 % |
0 |
0.00 % |
274 |
0.00 % |
| fs60,mq40 |
158 |
0.00 % |
0 |
0.00 % |
158 |
0.00 % |
| qd2,fs60 |
102 |
0.00 % |
0 |
0.00 % |
102 |
0.00 % |
| fs60 |
46 |
0.00 % |
0 |
0.00 % |
46 |
0.00 % |
| q20,qd2,fs60,mq40 |
28 |
0.00 % |
0 |
0.00 % |
28 |
0.00 % |
| q20,qd2,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
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 |
3576192 |
25.94 % |
| Transition |
G>A |
All |
1500021 |
10.88 % |
| Transition |
T>C |
All |
3238047 |
23.49 % |
| Transition |
C>T |
All |
1527518 |
11.08 % |
| Transversion |
A>C |
All |
260302 |
1.89 % |
| Transversion |
C>A |
All |
936416 |
6.79 % |
| Transversion |
T>G |
All |
294345 |
2.14 % |
| Transversion |
G>T |
All |
896580 |
6.50 % |
| Transversion |
A>T |
All |
502777 |
3.65 % |
| Transversion |
T>A |
All |
529306 |
3.84 % |
| Transversion |
C>G |
All |
273359 |
1.98 % |
| Transversion |
G>C |
All |
249664 |
1.81 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
354261 |
16.27 % |
| Transition |
G>A |
Passed |
333459 |
15.31 % |
| Transition |
T>C |
Passed |
370983 |
17.04 % |
| Transition |
C>T |
Passed |
345040 |
15.84 % |
| Transversion |
A>C |
Passed |
94452 |
4.34 % |
| Transversion |
C>A |
Passed |
105552 |
4.85 % |
| Transversion |
T>G |
Passed |
94805 |
4.35 % |
| Transversion |
G>T |
Passed |
105272 |
4.83 % |
| Transversion |
A>T |
Passed |
94036 |
4.32 % |
| Transversion |
T>A |
Passed |
94285 |
4.33 % |
| Transversion |
C>G |
Passed |
92865 |
4.26 % |
| Transversion |
G>C |
Passed |
92683 |
4.26 % |
| |
|
|
|
|
| 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 |
2.50 |
9841778 |
3942749 |
| Passed |
1.81 |
1403743 |
773950 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |