/EXTERNAL McGill EMC/variants/K006128_1_lane_gembs
BACK
SAMPLE K006128_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1137970745 |
145314986 |
12.77 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1137970745 |
100% |
1122846162 |
98.67 % |
15124583 |
1.33 % |
| |
|
|
|
|
|
|
| Passed |
150930823 |
13.26 % |
144172408 |
12.84 % |
6758415 |
4.48 % |
| Filtered |
987039922 |
86.74 % |
978673754 |
87.16 % |
8366168 |
5.54 % |
| |
|
|
|
|
|
|
| q20 |
941844888 |
95.42 % |
938630329 |
95.91 % |
3214559 |
38.42 % |
| q20,qd2 |
20746690 |
2.10 % |
15894759 |
1.62 % |
4851931 |
57.99 % |
| q20,mq40 |
18702357 |
1.89 % |
18610336 |
1.90 % |
92021 |
1.10 % |
| q20,qd2,mq40 |
5367643 |
0.54 % |
5297472 |
0.54 % |
70171 |
0.84 % |
| mq40 |
344573 |
0.03 % |
211948 |
0.02 % |
132625 |
1.59 % |
| qd2 |
22093 |
0.00 % |
19771 |
0.00 % |
2322 |
0.03 % |
| qd2,mq40 |
11487 |
0.00 % |
9139 |
0.00 % |
2348 |
0.03 % |
| qd2,fs60,mq40 |
91 |
0.00 % |
0 |
0.00 % |
91 |
0.00 % |
| qd2,fs60 |
46 |
0.00 % |
0 |
0.00 % |
46 |
0.00 % |
| fs60,mq40 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,qd2,fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
4722006 |
27.80 % |
| Transition |
G>A |
All |
1032911 |
6.08 % |
| Transition |
T>C |
All |
4253717 |
25.04 % |
| Transition |
C>T |
All |
1040327 |
6.12 % |
| Transversion |
A>C |
All |
343402 |
2.02 % |
| Transversion |
C>A |
All |
1377667 |
8.11 % |
| Transversion |
T>G |
All |
412765 |
2.43 % |
| Transversion |
G>T |
All |
1307989 |
7.70 % |
| Transversion |
A>T |
All |
890409 |
5.24 % |
| Transversion |
T>A |
All |
954022 |
5.62 % |
| Transversion |
C>G |
All |
346345 |
2.04 % |
| Transversion |
G>C |
All |
306381 |
1.80 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
187273 |
14.73 % |
| Transition |
G>A |
Passed |
175659 |
13.82 % |
| Transition |
T>C |
Passed |
184448 |
14.51 % |
| Transition |
C>T |
Passed |
178101 |
14.01 % |
| Transversion |
A>C |
Passed |
67860 |
5.34 % |
| Transversion |
C>A |
Passed |
72292 |
5.69 % |
| Transversion |
T>G |
Passed |
68018 |
5.35 % |
| Transversion |
G>T |
Passed |
72254 |
5.68 % |
| Transversion |
A>T |
Passed |
64079 |
5.04 % |
| Transversion |
T>A |
Passed |
63943 |
5.03 % |
| Transversion |
C>G |
Passed |
68722 |
5.40 % |
| Transversion |
G>C |
Passed |
68849 |
5.41 % |
| |
|
|
|
|
| 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 |
1.86 |
11048961 |
5938980 |
| Passed |
1.33 |
725481 |
546017 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |