/EXTERNAL McGill EMC/variants/K006187_1_lane_gembs
BACK
SAMPLE K006187_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1133903198 |
294416104 |
25.96 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1133903198 |
100% |
1114170968 |
98.26 % |
19732230 |
1.74 % |
| |
|
|
|
|
|
|
| Passed |
297745392 |
26.26 % |
292807887 |
26.28 % |
4937505 |
1.66 % |
| Filtered |
836157806 |
73.74 % |
821363081 |
73.72 % |
14794725 |
4.97 % |
| |
|
|
|
|
|
|
| q20 |
776669440 |
92.89 % |
773374650 |
94.16 % |
3294790 |
22.27 % |
| q20,qd2 |
38154406 |
4.56 % |
27090461 |
3.30 % |
11063945 |
74.78 % |
| q20,mq40 |
15496380 |
1.85 % |
15362177 |
1.87 % |
134203 |
0.91 % |
| q20,qd2,mq40 |
4556671 |
0.54 % |
4424803 |
0.54 % |
131868 |
0.89 % |
| qd2 |
659401 |
0.08 % |
633016 |
0.08 % |
26385 |
0.18 % |
| mq40 |
603020 |
0.07 % |
463633 |
0.06 % |
139387 |
0.94 % |
| qd2,mq40 |
18064 |
0.00 % |
14341 |
0.00 % |
3723 |
0.03 % |
| qd2,fs60,mq40 |
226 |
0.00 % |
0 |
0.00 % |
226 |
0.00 % |
| qd2,fs60 |
96 |
0.00 % |
0 |
0.00 % |
96 |
0.00 % |
| fs60,mq40 |
71 |
0.00 % |
0 |
0.00 % |
71 |
0.00 % |
| fs60 |
17 |
0.00 % |
0 |
0.00 % |
17 |
0.00 % |
| q20,qd2,fs60,mq40 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,qd2,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
3765535 |
17.40 % |
| Transition |
G>A |
All |
1225542 |
5.66 % |
| Transition |
T>C |
All |
3400761 |
15.72 % |
| Transition |
C>T |
All |
1243937 |
5.75 % |
| Transversion |
A>C |
All |
478014 |
2.21 % |
| Transversion |
C>A |
All |
4445284 |
20.54 % |
| Transversion |
T>G |
All |
521907 |
2.41 % |
| Transversion |
G>T |
All |
4477963 |
20.69 % |
| Transversion |
A>T |
All |
614719 |
2.84 % |
| Transversion |
T>A |
All |
663154 |
3.06 % |
| Transversion |
C>G |
All |
415834 |
1.92 % |
| Transversion |
G>C |
All |
386027 |
1.78 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
406993 |
20.98 % |
| Transition |
G>A |
Passed |
245627 |
12.66 % |
| Transition |
T>C |
Passed |
381852 |
19.69 % |
| Transition |
C>T |
Passed |
247243 |
12.75 % |
| Transversion |
A>C |
Passed |
79742 |
4.11 % |
| Transversion |
C>A |
Passed |
90011 |
4.64 % |
| Transversion |
T>G |
Passed |
80826 |
4.17 % |
| Transversion |
G>T |
Passed |
88977 |
4.59 % |
| Transversion |
A>T |
Passed |
79492 |
4.10 % |
| Transversion |
T>A |
Passed |
80244 |
4.14 % |
| Transversion |
C>G |
Passed |
79528 |
4.10 % |
| Transversion |
G>C |
Passed |
79088 |
4.08 % |
| |
|
|
|
|
| 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 |
0.80 |
9635775 |
12002902 |
| Passed |
1.95 |
1281715 |
657908 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |