/EXTERNAL McGill EMC/variants/K006171_1_lane_gembs
BACK
SAMPLE K006171_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1189017083 |
538520133 |
45.29 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1189017083 |
100% |
1118478468 |
94.07 % |
70538615 |
5.93 % |
| |
|
|
|
|
|
|
| Passed |
549899007 |
46.25 % |
530541884 |
47.43 % |
19357123 |
3.52 % |
| Filtered |
639118076 |
53.75 % |
587936584 |
52.57 % |
51181492 |
9.31 % |
| |
|
|
|
|
|
|
| q20 |
524616724 |
82.08 % |
516626987 |
87.87 % |
7989737 |
15.61 % |
| q20,qd2 |
51906407 |
8.12 % |
19764079 |
3.36 % |
32142328 |
62.80 % |
| q20,mq40 |
25496544 |
3.99 % |
24303496 |
4.13 % |
1193048 |
2.33 % |
| mq40 |
22525084 |
3.52 % |
17682850 |
3.01 % |
4842234 |
9.46 % |
| q20,qd2,mq40 |
9406957 |
1.47 % |
5629655 |
0.96 % |
3777302 |
7.38 % |
| qd2 |
4529368 |
0.71 % |
3512493 |
0.60 % |
1016875 |
1.99 % |
| qd2,mq40 |
635492 |
0.10 % |
417024 |
0.07 % |
218468 |
0.43 % |
| qd2,fs60,mq40 |
906 |
0.00 % |
0 |
0.00 % |
906 |
0.00 % |
| fs60,mq40 |
300 |
0.00 % |
0 |
0.00 % |
300 |
0.00 % |
| qd2,fs60 |
154 |
0.00 % |
0 |
0.00 % |
154 |
0.00 % |
| fs60 |
68 |
0.00 % |
0 |
0.00 % |
68 |
0.00 % |
| q20,qd2,fs60,mq40 |
48 |
0.00 % |
0 |
0.00 % |
48 |
0.00 % |
| q20,qd2,fs60 |
24 |
0.00 % |
0 |
0.00 % |
24 |
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 |
17633487 |
24.30 % |
| Transition |
G>A |
All |
7706501 |
10.62 % |
| Transition |
T>C |
All |
17008593 |
23.44 % |
| Transition |
C>T |
All |
7131330 |
9.83 % |
| Transversion |
A>C |
All |
1273985 |
1.76 % |
| Transversion |
C>A |
All |
5898177 |
8.13 % |
| Transversion |
T>G |
All |
1361136 |
1.88 % |
| Transversion |
G>T |
All |
5987298 |
8.25 % |
| Transversion |
A>T |
All |
3014196 |
4.15 % |
| Transversion |
T>A |
All |
2900682 |
4.00 % |
| Transversion |
C>G |
All |
1361521 |
1.88 % |
| Transversion |
G>C |
All |
1298800 |
1.79 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2060446 |
24.36 % |
| Transition |
G>A |
Passed |
1065093 |
12.59 % |
| Transition |
T>C |
Passed |
1897560 |
22.43 % |
| Transition |
C>T |
Passed |
984102 |
11.63 % |
| Transversion |
A>C |
Passed |
342914 |
4.05 % |
| Transversion |
C>A |
Passed |
264050 |
3.12 % |
| Transversion |
T>G |
Passed |
352438 |
4.17 % |
| Transversion |
G>T |
Passed |
257325 |
3.04 % |
| Transversion |
A>T |
Passed |
263385 |
3.11 % |
| Transversion |
T>A |
Passed |
271162 |
3.21 % |
| Transversion |
C>G |
Passed |
353811 |
4.18 % |
| Transversion |
G>C |
Passed |
347688 |
4.11 % |
| |
|
|
|
|
| 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 |
2.14 |
49479911 |
23095795 |
| Passed |
2.45 |
6007201 |
2452773 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |