/EXTERNAL McGill EMC/variants/K006176_1_lane_gembs
BACK
SAMPLE K006176_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1150309073 |
863570824 |
75.07 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1150309073 |
100% |
1135813793 |
98.74 % |
14495280 |
1.26 % |
| |
|
|
|
|
|
|
| Passed |
865100762 |
75.21 % |
861225804 |
75.82 % |
3874958 |
0.45 % |
| Filtered |
285208311 |
24.79 % |
274587989 |
24.18 % |
10620322 |
1.23 % |
| |
|
|
|
|
|
|
| q20 |
246789234 |
86.53 % |
245103405 |
89.26 % |
1685829 |
15.87 % |
| q20,mq40 |
16771336 |
5.88 % |
16654482 |
6.07 % |
116854 |
1.10 % |
| q20,qd2 |
14639174 |
5.13 % |
6182656 |
2.25 % |
8456518 |
79.63 % |
| q20,qd2,mq40 |
3627876 |
1.27 % |
3494731 |
1.27 % |
133145 |
1.25 % |
| mq40 |
2415899 |
0.85 % |
2235005 |
0.81 % |
180894 |
1.70 % |
| qd2 |
932883 |
0.33 % |
892514 |
0.33 % |
40369 |
0.38 % |
| qd2,mq40 |
31247 |
0.01 % |
25196 |
0.01 % |
6051 |
0.06 % |
| qd2,fs60,mq40 |
336 |
0.00 % |
0 |
0.00 % |
336 |
0.00 % |
| fs60,mq40 |
167 |
0.00 % |
0 |
0.00 % |
167 |
0.00 % |
| qd2,fs60 |
97 |
0.00 % |
0 |
0.00 % |
97 |
0.00 % |
| q20,qd2,fs60,mq40 |
29 |
0.00 % |
0 |
0.00 % |
29 |
0.00 % |
| fs60 |
28 |
0.00 % |
0 |
0.00 % |
28 |
0.00 % |
| q20,qd2,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
5358560 |
33.18 % |
| Transition |
G>A |
All |
1365326 |
8.45 % |
| Transition |
T>C |
All |
5209339 |
32.26 % |
| Transition |
C>T |
All |
1244488 |
7.71 % |
| Transversion |
A>C |
All |
221305 |
1.37 % |
| Transversion |
C>A |
All |
660578 |
4.09 % |
| Transversion |
T>G |
All |
227062 |
1.41 % |
| Transversion |
G>T |
All |
625619 |
3.87 % |
| Transversion |
A>T |
All |
395175 |
2.45 % |
| Transversion |
T>A |
All |
397794 |
2.46 % |
| Transversion |
C>G |
All |
223281 |
1.38 % |
| Transversion |
G>C |
All |
220207 |
1.36 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
561508 |
17.00 % |
| Transition |
G>A |
Passed |
530423 |
16.06 % |
| Transition |
T>C |
Passed |
566038 |
17.13 % |
| Transition |
C>T |
Passed |
538086 |
16.29 % |
| Transversion |
A>C |
Passed |
137981 |
4.18 % |
| Transversion |
C>A |
Passed |
147792 |
4.47 % |
| Transversion |
T>G |
Passed |
138615 |
4.20 % |
| Transversion |
G>T |
Passed |
147587 |
4.47 % |
| Transversion |
A>T |
Passed |
126794 |
3.84 % |
| Transversion |
T>A |
Passed |
125791 |
3.81 % |
| Transversion |
C>G |
Passed |
141233 |
4.28 % |
| Transversion |
G>C |
Passed |
141776 |
4.29 % |
| |
|
|
|
|
| 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 |
4.44 |
13177713 |
2971021 |
| Passed |
1.98 |
2196055 |
1107569 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |