/EXTERNAL McGill EMC/variants/K006147_1_lane_gembs
BACK
SAMPLE K006147_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1160692339 |
708479083 |
61.04 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1160692339 |
100% |
1138136964 |
98.06 % |
22555375 |
1.94 % |
| |
|
|
|
|
|
|
| Passed |
712575466 |
61.39 % |
706363858 |
62.06 % |
6211608 |
0.87 % |
| Filtered |
448116873 |
38.61 % |
431773106 |
37.94 % |
16343767 |
2.29 % |
| |
|
|
|
|
|
|
| q20 |
405088326 |
90.40 % |
401747656 |
93.05 % |
3340670 |
20.44 % |
| q20,qd2 |
22678853 |
5.06 % |
10149241 |
2.35 % |
12529612 |
76.66 % |
| q20,mq40 |
13773768 |
3.07 % |
13668873 |
3.17 % |
104895 |
0.64 % |
| q20,qd2,mq40 |
3308261 |
0.74 % |
3170958 |
0.73 % |
137303 |
0.84 % |
| mq40 |
1654947 |
0.37 % |
1477991 |
0.34 % |
176956 |
1.08 % |
| qd2 |
1576398 |
0.35 % |
1529589 |
0.35 % |
46809 |
0.29 % |
| qd2,mq40 |
35308 |
0.01 % |
28798 |
0.01 % |
6510 |
0.04 % |
| qd2,fs60,mq40 |
499 |
0.00 % |
0 |
0.00 % |
499 |
0.00 % |
| fs60,mq40 |
238 |
0.00 % |
0 |
0.00 % |
238 |
0.00 % |
| qd2,fs60 |
157 |
0.00 % |
0 |
0.00 % |
157 |
0.00 % |
| fs60 |
61 |
0.00 % |
0 |
0.00 % |
61 |
0.00 % |
| q20,qd2,fs60,mq40 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| q20,qd2,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
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 |
8431057 |
34.72 % |
| Transition |
G>A |
All |
1159059 |
4.77 % |
| Transition |
T>C |
All |
8043652 |
33.12 % |
| Transition |
C>T |
All |
1183115 |
4.87 % |
| Transversion |
A>C |
All |
244888 |
1.01 % |
| Transversion |
C>A |
All |
1762496 |
7.26 % |
| Transversion |
T>G |
All |
265937 |
1.10 % |
| Transversion |
G>T |
All |
1743523 |
7.18 % |
| Transversion |
A>T |
All |
471524 |
1.94 % |
| Transversion |
T>A |
All |
479000 |
1.97 % |
| Transversion |
C>G |
All |
257553 |
1.06 % |
| Transversion |
G>C |
All |
242721 |
1.00 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
516426 |
17.75 % |
| Transition |
G>A |
Passed |
443081 |
15.23 % |
| Transition |
T>C |
Passed |
510249 |
17.54 % |
| Transition |
C>T |
Passed |
449324 |
15.44 % |
| Transversion |
A>C |
Passed |
123465 |
4.24 % |
| Transversion |
C>A |
Passed |
134226 |
4.61 % |
| Transversion |
T>G |
Passed |
124464 |
4.28 % |
| Transversion |
G>T |
Passed |
133599 |
4.59 % |
| Transversion |
A>T |
Passed |
112829 |
3.88 % |
| Transversion |
T>A |
Passed |
112446 |
3.86 % |
| Transversion |
C>G |
Passed |
124913 |
4.29 % |
| Transversion |
G>C |
Passed |
124804 |
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 |
3.44 |
18816883 |
5467642 |
| Passed |
1.94 |
1919080 |
990746 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |