/EXTERNAL McGill EMC/variants/K006165_1_lane_gembs
BACK
SAMPLE K006165_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1136450963 |
124425976 |
10.95 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1136450963 |
100% |
1123102876 |
98.83 % |
13348087 |
1.17 % |
| |
|
|
|
|
|
|
| Passed |
130201200 |
11.46 % |
123358825 |
10.98 % |
6842375 |
5.26 % |
| Filtered |
1006249763 |
88.54 % |
999744051 |
89.02 % |
6505712 |
5.00 % |
| |
|
|
|
|
|
|
| q20 |
962664106 |
95.67 % |
960086782 |
96.03 % |
2577324 |
39.62 % |
| q20,qd2 |
20155599 |
2.00 % |
16484091 |
1.65 % |
3671508 |
56.44 % |
| q20,mq40 |
17935018 |
1.78 % |
17862836 |
1.79 % |
72182 |
1.11 % |
| q20,qd2,mq40 |
5161899 |
0.51 % |
5100449 |
0.51 % |
61450 |
0.94 % |
| mq40 |
303952 |
0.03 % |
185335 |
0.02 % |
118617 |
1.82 % |
| qd2 |
18274 |
0.00 % |
16103 |
0.00 % |
2171 |
0.03 % |
| qd2,mq40 |
10709 |
0.00 % |
8455 |
0.00 % |
2254 |
0.03 % |
| qd2,fs60,mq40 |
93 |
0.00 % |
0 |
0.00 % |
93 |
0.00 % |
| qd2,fs60 |
50 |
0.00 % |
0 |
0.00 % |
50 |
0.00 % |
| fs60,mq40 |
43 |
0.00 % |
0 |
0.00 % |
43 |
0.00 % |
| q20,qd2,fs60,mq40 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
4621360 |
30.38 % |
| Transition |
G>A |
All |
830307 |
5.46 % |
| Transition |
T>C |
All |
4119355 |
27.08 % |
| Transition |
C>T |
All |
850188 |
5.59 % |
| Transversion |
A>C |
All |
230644 |
1.52 % |
| Transversion |
C>A |
All |
1009239 |
6.63 % |
| Transversion |
T>G |
All |
312371 |
2.05 % |
| Transversion |
G>T |
All |
943986 |
6.21 % |
| Transversion |
A>T |
All |
847199 |
5.57 % |
| Transversion |
T>A |
All |
932199 |
6.13 % |
| Transversion |
C>G |
All |
280968 |
1.85 % |
| Transversion |
G>C |
All |
233857 |
1.54 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
168534 |
14.35 % |
| Transition |
G>A |
Passed |
159542 |
13.58 % |
| Transition |
T>C |
Passed |
170699 |
14.53 % |
| Transition |
C>T |
Passed |
163207 |
13.89 % |
| Transversion |
A>C |
Passed |
63949 |
5.44 % |
| Transversion |
C>A |
Passed |
67638 |
5.76 % |
| Transversion |
T>G |
Passed |
63907 |
5.44 % |
| Transversion |
G>T |
Passed |
67660 |
5.76 % |
| Transversion |
A>T |
Passed |
59420 |
5.06 % |
| Transversion |
T>A |
Passed |
59375 |
5.05 % |
| Transversion |
C>G |
Passed |
65316 |
5.56 % |
| Transversion |
G>C |
Passed |
65440 |
5.57 % |
| |
|
|
|
|
| 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 |
2.18 |
10421210 |
4790463 |
| Passed |
1.29 |
661982 |
512705 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |