/EXTERNAL McGill EMC/variants/K006194_1_lane_gembs
BACK
SAMPLE K006194_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1158283645 |
577669234 |
49.87 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1158283645 |
100% |
1132240134 |
97.75 % |
26043511 |
2.25 % |
| |
|
|
|
|
|
|
| Passed |
582415844 |
50.28 % |
574857705 |
50.77 % |
7558139 |
1.30 % |
| Filtered |
575867801 |
49.72 % |
557382429 |
49.23 % |
18485372 |
3.17 % |
| |
|
|
|
|
|
|
| q20 |
525944183 |
91.33 % |
522312578 |
93.71 % |
3631605 |
19.65 % |
| q20,qd2 |
27866138 |
4.84 % |
13500412 |
2.42 % |
14365726 |
77.71 % |
| q20,mq40 |
16160836 |
2.81 % |
16049663 |
2.88 % |
111173 |
0.60 % |
| q20,qd2,mq40 |
3715925 |
0.65 % |
3561024 |
0.64 % |
154901 |
0.84 % |
| mq40 |
1092924 |
0.19 % |
909442 |
0.16 % |
183482 |
0.99 % |
| qd2 |
1070409 |
0.19 % |
1035619 |
0.19 % |
34790 |
0.19 % |
| qd2,mq40 |
16972 |
0.00 % |
13691 |
0.00 % |
3281 |
0.02 % |
| qd2,fs60,mq40 |
198 |
0.00 % |
0 |
0.00 % |
198 |
0.00 % |
| qd2,fs60 |
105 |
0.00 % |
0 |
0.00 % |
105 |
0.00 % |
| fs60,mq40 |
80 |
0.00 % |
0 |
0.00 % |
80 |
0.00 % |
| fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,qd2,fs60,mq40 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
8422026 |
30.89 % |
| Transition |
G>A |
All |
1240007 |
4.55 % |
| Transition |
T>C |
All |
8361496 |
30.67 % |
| Transition |
C>T |
All |
1238833 |
4.54 % |
| Transversion |
A>C |
All |
259109 |
0.95 % |
| Transversion |
C>A |
All |
2835863 |
10.40 % |
| Transversion |
T>G |
All |
266354 |
0.98 % |
| Transversion |
G>T |
All |
2825600 |
10.36 % |
| Transversion |
A>T |
All |
610083 |
2.24 % |
| Transversion |
T>A |
All |
599180 |
2.20 % |
| Transversion |
C>G |
All |
306737 |
1.12 % |
| Transversion |
G>C |
All |
300824 |
1.10 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
538886 |
16.79 % |
| Transition |
G>A |
Passed |
478017 |
14.89 % |
| Transition |
T>C |
Passed |
539762 |
16.82 % |
| Transition |
C>T |
Passed |
483326 |
15.06 % |
| Transversion |
A>C |
Passed |
144377 |
4.50 % |
| Transversion |
C>A |
Passed |
156561 |
4.88 % |
| Transversion |
T>G |
Passed |
144657 |
4.51 % |
| Transversion |
G>T |
Passed |
156561 |
4.88 % |
| Transversion |
A>T |
Passed |
138620 |
4.32 % |
| Transversion |
T>A |
Passed |
137852 |
4.29 % |
| Transversion |
C>G |
Passed |
145426 |
4.53 % |
| Transversion |
G>C |
Passed |
145934 |
4.55 % |
| |
|
|
|
|
| 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 |
2.41 |
19262362 |
8003750 |
| Passed |
1.74 |
2039991 |
1169988 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |