/EXTERNAL McGill EMC/variants/K006200_1_lane_gembs
BACK
SAMPLE K006200_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1159128057 |
616091645 |
53.15 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1159128057 |
100% |
1131907802 |
97.65 % |
27220255 |
2.35 % |
| |
|
|
|
|
|
|
| Passed |
620504728 |
53.53 % |
613167195 |
54.17 % |
7337533 |
1.18 % |
| Filtered |
538623329 |
46.47 % |
518740607 |
45.83 % |
19882722 |
3.20 % |
| |
|
|
|
|
|
|
| q20 |
485674617 |
90.17 % |
482104582 |
92.94 % |
3570035 |
17.96 % |
| q20,qd2 |
30355361 |
5.64 % |
14565913 |
2.81 % |
15789448 |
79.41 % |
| q20,mq40 |
16400117 |
3.04 % |
16283063 |
3.14 % |
117054 |
0.59 % |
| q20,qd2,mq40 |
3660497 |
0.68 % |
3476958 |
0.67 % |
183539 |
0.92 % |
| mq40 |
1264354 |
0.23 % |
1075943 |
0.21 % |
188411 |
0.95 % |
| qd2 |
1251216 |
0.23 % |
1220620 |
0.24 % |
30596 |
0.15 % |
| qd2,mq40 |
16755 |
0.00 % |
13528 |
0.00 % |
3227 |
0.02 % |
| qd2,fs60,mq40 |
216 |
0.00 % |
0 |
0.00 % |
216 |
0.00 % |
| qd2,fs60 |
88 |
0.00 % |
0 |
0.00 % |
88 |
0.00 % |
| fs60,mq40 |
72 |
0.00 % |
0 |
0.00 % |
72 |
0.00 % |
| fs60 |
17 |
0.00 % |
0 |
0.00 % |
17 |
0.00 % |
| q20,qd2,fs60,mq40 |
16 |
0.00 % |
0 |
0.00 % |
16 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
8363495 |
29.45 % |
| Transition |
G>A |
All |
1272142 |
4.48 % |
| Transition |
T>C |
All |
8276255 |
29.14 % |
| Transition |
C>T |
All |
1275865 |
4.49 % |
| Transversion |
A>C |
All |
261166 |
0.92 % |
| Transversion |
C>A |
All |
3404193 |
11.99 % |
| Transversion |
T>G |
All |
269801 |
0.95 % |
| Transversion |
G>T |
All |
3387167 |
11.93 % |
| Transversion |
A>T |
All |
636666 |
2.24 % |
| Transversion |
T>A |
All |
627104 |
2.21 % |
| Transversion |
C>G |
All |
316291 |
1.11 % |
| Transversion |
G>C |
All |
308120 |
1.08 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
555612 |
16.65 % |
| Transition |
G>A |
Passed |
500924 |
15.01 % |
| Transition |
T>C |
Passed |
556194 |
16.67 % |
| Transition |
C>T |
Passed |
506656 |
15.18 % |
| Transversion |
A>C |
Passed |
150299 |
4.50 % |
| Transversion |
C>A |
Passed |
161590 |
4.84 % |
| Transversion |
T>G |
Passed |
150132 |
4.50 % |
| Transversion |
G>T |
Passed |
162873 |
4.88 % |
| Transversion |
A>T |
Passed |
142568 |
4.27 % |
| Transversion |
T>A |
Passed |
142353 |
4.27 % |
| Transversion |
C>G |
Passed |
153711 |
4.61 % |
| Transversion |
G>C |
Passed |
153871 |
4.61 % |
| |
|
|
|
|
| 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 |
2.08 |
19187757 |
9210508 |
| Passed |
1.74 |
2119386 |
1217397 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |