/EXTERNAL McGill EMC/variants/K006145_1_lane_gembs
BACK
SAMPLE K006145_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1134313881 |
218583022 |
19.27 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1134313881 |
100% |
1122344395 |
98.94 % |
11969486 |
1.06 % |
| |
|
|
|
|
|
|
| Passed |
221612225 |
19.54 % |
217470659 |
19.38 % |
4141566 |
1.87 % |
| Filtered |
912701656 |
80.46 % |
904873736 |
80.62 % |
7827920 |
3.53 % |
| |
|
|
|
|
|
|
| q20 |
859595504 |
94.18 % |
856727628 |
94.68 % |
2867876 |
36.64 % |
| q20,qd2 |
32696727 |
3.58 % |
28012448 |
3.10 % |
4684279 |
59.84 % |
| q20,mq40 |
15198575 |
1.67 % |
15108757 |
1.67 % |
89818 |
1.15 % |
| q20,qd2,mq40 |
4572703 |
0.50 % |
4503890 |
0.50 % |
68813 |
0.88 % |
| mq40 |
405029 |
0.04 % |
300738 |
0.03 % |
104291 |
1.33 % |
| qd2 |
208647 |
0.02 % |
200632 |
0.02 % |
8015 |
0.10 % |
| qd2,mq40 |
23939 |
0.00 % |
19643 |
0.00 % |
4296 |
0.05 % |
| qd2,fs60,mq40 |
294 |
0.00 % |
0 |
0.00 % |
294 |
0.00 % |
| fs60,mq40 |
122 |
0.00 % |
0 |
0.00 % |
122 |
0.00 % |
| qd2,fs60 |
86 |
0.00 % |
0 |
0.00 % |
86 |
0.00 % |
| q20,qd2,fs60,mq40 |
20 |
0.00 % |
0 |
0.00 % |
20 |
0.00 % |
| fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3591559 |
25.91 % |
| Transition |
G>A |
All |
892423 |
6.44 % |
| Transition |
T>C |
All |
2945265 |
21.25 % |
| Transition |
C>T |
All |
929915 |
6.71 % |
| Transversion |
A>C |
All |
373071 |
2.69 % |
| Transversion |
C>A |
All |
1406161 |
10.14 % |
| Transversion |
T>G |
All |
457896 |
3.30 % |
| Transversion |
G>T |
All |
1353952 |
9.77 % |
| Transversion |
A>T |
All |
593567 |
4.28 % |
| Transversion |
T>A |
All |
666423 |
4.81 % |
| Transversion |
C>G |
All |
351144 |
2.53 % |
| Transversion |
G>C |
All |
301903 |
2.18 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
206820 |
15.28 % |
| Transition |
G>A |
Passed |
201094 |
14.86 % |
| Transition |
T>C |
Passed |
208100 |
15.38 % |
| Transition |
C>T |
Passed |
205314 |
15.17 % |
| Transversion |
A>C |
Passed |
65743 |
4.86 % |
| Transversion |
C>A |
Passed |
71578 |
5.29 % |
| Transversion |
T>G |
Passed |
66494 |
4.91 % |
| Transversion |
G>T |
Passed |
71349 |
5.27 % |
| Transversion |
A>T |
Passed |
63247 |
4.67 % |
| Transversion |
T>A |
Passed |
63673 |
4.71 % |
| Transversion |
C>G |
Passed |
64667 |
4.78 % |
| Transversion |
G>C |
Passed |
65183 |
4.82 % |
| |
|
|
|
|
| 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 |
1.52 |
8359162 |
5504117 |
| Passed |
1.54 |
821328 |
531934 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |