/EXTERNAL McGill EMC/variants/K006205_1_lane_gembs
BACK
SAMPLE K006205_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1183518566 |
973920343 |
82.29 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1183518566 |
100% |
1148723091 |
97.06 % |
34795475 |
2.94 % |
| |
|
|
|
|
|
|
| Passed |
976178918 |
82.48 % |
967312419 |
84.21 % |
8866499 |
0.91 % |
| Filtered |
207339648 |
17.52 % |
181410672 |
15.79 % |
25928976 |
2.66 % |
| |
|
|
|
|
|
|
| q20 |
144389252 |
69.64 % |
141481726 |
77.99 % |
2907526 |
11.21 % |
| q20,qd2 |
33199185 |
16.01 % |
13499596 |
7.44 % |
19699589 |
75.98 % |
| q20,mq40 |
12746180 |
6.15 % |
12536206 |
6.91 % |
209974 |
0.81 % |
| qd2 |
10298590 |
4.97 % |
7823289 |
4.31 % |
2475301 |
9.55 % |
| mq40 |
3740512 |
1.80 % |
3451455 |
1.90 % |
289057 |
1.11 % |
| q20,qd2,mq40 |
2905461 |
1.40 % |
2569101 |
1.42 % |
336360 |
1.30 % |
| qd2,mq40 |
59571 |
0.03 % |
49299 |
0.03 % |
10272 |
0.04 % |
| qd2,fs60,mq40 |
376 |
0.00 % |
0 |
0.00 % |
376 |
0.00 % |
| qd2,fs60 |
226 |
0.00 % |
0 |
0.00 % |
226 |
0.00 % |
| fs60,mq40 |
154 |
0.00 % |
0 |
0.00 % |
154 |
0.00 % |
| fs60 |
99 |
0.00 % |
0 |
0.00 % |
99 |
0.00 % |
| q20,qd2,fs60,mq40 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| q20,qd2,fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
12800982 |
35.06 % |
| Transition |
G>A |
All |
1476791 |
4.04 % |
| Transition |
T>C |
All |
12116085 |
33.19 % |
| Transition |
C>T |
All |
1524473 |
4.18 % |
| Transversion |
A>C |
All |
357104 |
0.98 % |
| Transversion |
C>A |
All |
2727069 |
7.47 % |
| Transversion |
T>G |
All |
387586 |
1.06 % |
| Transversion |
G>T |
All |
2668611 |
7.31 % |
| Transversion |
A>T |
All |
755611 |
2.07 % |
| Transversion |
T>A |
All |
791436 |
2.17 % |
| Transversion |
C>G |
All |
469394 |
1.29 % |
| Transversion |
G>C |
All |
435014 |
1.19 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2632858 |
34.13 % |
| Transition |
G>A |
Passed |
602483 |
7.81 % |
| Transition |
T>C |
Passed |
2536988 |
32.88 % |
| Transition |
C>T |
Passed |
602742 |
7.81 % |
| Transversion |
A>C |
Passed |
162919 |
2.11 % |
| Transversion |
C>A |
Passed |
169084 |
2.19 % |
| Transversion |
T>G |
Passed |
165747 |
2.15 % |
| Transversion |
G>T |
Passed |
168729 |
2.19 % |
| Transversion |
A>T |
Passed |
150038 |
1.94 % |
| Transversion |
T>A |
Passed |
151043 |
1.96 % |
| Transversion |
C>G |
Passed |
187617 |
2.43 % |
| Transversion |
G>C |
Passed |
184962 |
2.40 % |
| |
|
|
|
|
| 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 |
3.25 |
27918331 |
8591825 |
| Passed |
4.76 |
6375071 |
1340139 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |