/EXTERNAL McGill EMC/variants/K006140_1_lane_gembs
BACK
SAMPLE K006140_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157426312 |
854940348 |
73.87 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157426312 |
100% |
1141048056 |
98.58 % |
16378256 |
1.42 % |
| |
|
|
|
|
|
|
| Passed |
856605635 |
74.01 % |
851632491 |
74.64 % |
4973144 |
0.58 % |
| Filtered |
300820677 |
25.99 % |
289415565 |
25.36 % |
11405112 |
1.33 % |
| |
|
|
|
|
|
|
| q20 |
264452196 |
87.91 % |
262379503 |
90.66 % |
2072693 |
18.17 % |
| q20,qd2 |
15623541 |
5.19 % |
6754263 |
2.33 % |
8869278 |
77.77 % |
| q20,mq40 |
14457792 |
4.81 % |
14342723 |
4.96 % |
115069 |
1.01 % |
| q20,qd2,mq40 |
3641358 |
1.21 % |
3524540 |
1.22 % |
116818 |
1.02 % |
| mq40 |
1493174 |
0.50 % |
1326948 |
0.46 % |
166226 |
1.46 % |
| qd2 |
1119238 |
0.37 % |
1061407 |
0.37 % |
57831 |
0.51 % |
| qd2,mq40 |
32577 |
0.01 % |
26181 |
0.01 % |
6396 |
0.06 % |
| qd2,fs60,mq40 |
450 |
0.00 % |
0 |
0.00 % |
450 |
0.00 % |
| fs60,mq40 |
191 |
0.00 % |
0 |
0.00 % |
191 |
0.00 % |
| qd2,fs60 |
96 |
0.00 % |
0 |
0.00 % |
96 |
0.00 % |
| q20,qd2,fs60,mq40 |
32 |
0.00 % |
0 |
0.00 % |
32 |
0.00 % |
| fs60 |
29 |
0.00 % |
0 |
0.00 % |
29 |
0.00 % |
| q20,qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
5731712 |
32.73 % |
| Transition |
G>A |
All |
1386686 |
7.92 % |
| Transition |
T>C |
All |
5619669 |
32.09 % |
| Transition |
C>T |
All |
1388307 |
7.93 % |
| Transversion |
A>C |
All |
270866 |
1.55 % |
| Transversion |
C>A |
All |
631605 |
3.61 % |
| Transversion |
T>G |
All |
277639 |
1.59 % |
| Transversion |
G>T |
All |
621536 |
3.55 % |
| Transversion |
A>T |
All |
516578 |
2.95 % |
| Transversion |
T>A |
All |
516790 |
2.95 % |
| Transversion |
C>G |
All |
279044 |
1.59 % |
| Transversion |
G>C |
All |
273695 |
1.56 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
644417 |
16.59 % |
| Transition |
G>A |
Passed |
612188 |
15.76 % |
| Transition |
T>C |
Passed |
645119 |
16.61 % |
| Transition |
C>T |
Passed |
613901 |
15.81 % |
| Transversion |
A>C |
Passed |
171456 |
4.41 % |
| Transversion |
C>A |
Passed |
178360 |
4.59 % |
| Transversion |
T>G |
Passed |
172366 |
4.44 % |
| Transversion |
G>T |
Passed |
179293 |
4.62 % |
| Transversion |
A>T |
Passed |
156335 |
4.03 % |
| Transversion |
T>A |
Passed |
156243 |
4.02 % |
| Transversion |
C>G |
Passed |
177036 |
4.56 % |
| Transversion |
G>C |
Passed |
177239 |
4.56 % |
| |
|
|
|
|
| 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 |
4.17 |
14126374 |
3387753 |
| Passed |
1.84 |
2515625 |
1368328 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |