/EXTERNAL McGill EMC/variants/K006163_1_lane_gembs
BACK
SAMPLE K006163_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1145071666 |
834089920 |
72.84 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1145071666 |
100% |
1135573483 |
99.17 % |
9498183 |
0.83 % |
| |
|
|
|
|
|
|
| Passed |
835225759 |
72.94 % |
831923608 |
73.26 % |
3302151 |
0.40 % |
| Filtered |
309845907 |
27.06 % |
303649875 |
26.74 % |
6196032 |
0.74 % |
| |
|
|
|
|
|
|
| q20 |
280402439 |
90.50 % |
279287337 |
91.98 % |
1115102 |
18.00 % |
| q20,qd2 |
11516534 |
3.72 % |
6799585 |
2.24 % |
4716949 |
76.13 % |
| q20,mq40 |
11066065 |
3.57 % |
10987533 |
3.62 % |
78532 |
1.27 % |
| q20,qd2,mq40 |
2712742 |
0.88 % |
2618587 |
0.86 % |
94155 |
1.52 % |
| qd2 |
2371770 |
0.77 % |
2322438 |
0.76 % |
49332 |
0.80 % |
| mq40 |
1734253 |
0.56 % |
1601398 |
0.53 % |
132855 |
2.14 % |
| qd2,mq40 |
40750 |
0.01 % |
32997 |
0.01 % |
7753 |
0.13 % |
| qd2,fs60,mq40 |
698 |
0.00 % |
0 |
0.00 % |
698 |
0.01 % |
| fs60,mq40 |
292 |
0.00 % |
0 |
0.00 % |
292 |
0.00 % |
| qd2,fs60 |
164 |
0.00 % |
0 |
0.00 % |
164 |
0.00 % |
| fs60 |
101 |
0.00 % |
0 |
0.00 % |
101 |
0.00 % |
| q20,qd2,fs60,mq40 |
66 |
0.00 % |
0 |
0.00 % |
66 |
0.00 % |
| q20,qd2,fs60 |
32 |
0.00 % |
0 |
0.00 % |
32 |
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 |
2949976 |
26.55 % |
| Transition |
G>A |
All |
1220055 |
10.98 % |
| Transition |
T>C |
All |
2812224 |
25.31 % |
| Transition |
C>T |
All |
1227735 |
11.05 % |
| Transversion |
A>C |
All |
208463 |
1.88 % |
| Transversion |
C>A |
All |
692187 |
6.23 % |
| Transversion |
T>G |
All |
213730 |
1.92 % |
| Transversion |
G>T |
All |
692230 |
6.23 % |
| Transversion |
A>T |
All |
333707 |
3.00 % |
| Transversion |
T>A |
All |
329473 |
2.96 % |
| Transversion |
C>G |
All |
217832 |
1.96 % |
| Transversion |
G>C |
All |
214510 |
1.93 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
506159 |
16.52 % |
| Transition |
G>A |
Passed |
501633 |
16.37 % |
| Transition |
T>C |
Passed |
509442 |
16.63 % |
| Transition |
C>T |
Passed |
507141 |
16.55 % |
| Transversion |
A>C |
Passed |
129214 |
4.22 % |
| Transversion |
C>A |
Passed |
139579 |
4.56 % |
| Transversion |
T>G |
Passed |
129246 |
4.22 % |
| Transversion |
G>T |
Passed |
138060 |
4.51 % |
| Transversion |
A>T |
Passed |
118755 |
3.88 % |
| Transversion |
T>A |
Passed |
118970 |
3.88 % |
| Transversion |
C>G |
Passed |
132829 |
4.34 % |
| Transversion |
G>C |
Passed |
132869 |
4.34 % |
| |
|
|
|
|
| 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 |
2.83 |
8209990 |
2902132 |
| Passed |
1.95 |
2024375 |
1039522 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |