/EXTERNAL McGill EMC/variants/K006155_1_lane_gembs
BACK
SAMPLE K006155_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1138052706 |
258500158 |
22.71 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1138052706 |
100% |
1109683837 |
97.51 % |
28368869 |
2.49 % |
| |
|
|
|
|
|
|
| Passed |
265136988 |
23.30 % |
257203993 |
23.18 % |
7932995 |
2.99 % |
| Filtered |
872915718 |
76.70 % |
852479844 |
76.82 % |
20435874 |
7.71 % |
| |
|
|
|
|
|
|
| q20 |
795463222 |
91.13 % |
790815983 |
92.77 % |
4647239 |
22.74 % |
| q20,qd2 |
52677620 |
6.03 % |
37360360 |
4.38 % |
15317260 |
74.95 % |
| q20,mq40 |
18072172 |
2.07 % |
17941814 |
2.10 % |
130358 |
0.64 % |
| q20,qd2,mq40 |
5560317 |
0.64 % |
5401168 |
0.63 % |
159149 |
0.78 % |
| qd2 |
574303 |
0.07 % |
551666 |
0.06 % |
22637 |
0.11 % |
| mq40 |
553574 |
0.06 % |
397152 |
0.05 % |
156422 |
0.77 % |
| qd2,mq40 |
14198 |
0.00 % |
11701 |
0.00 % |
2497 |
0.01 % |
| qd2,fs60,mq40 |
146 |
0.00 % |
0 |
0.00 % |
146 |
0.00 % |
| qd2,fs60 |
63 |
0.00 % |
0 |
0.00 % |
63 |
0.00 % |
| fs60,mq40 |
58 |
0.00 % |
0 |
0.00 % |
58 |
0.00 % |
| fs60 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| q20,qd2,fs60,mq40 |
17 |
0.00 % |
0 |
0.00 % |
17 |
0.00 % |
| q20,qd2,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
7733765 |
25.34 % |
| Transition |
G>A |
All |
1017542 |
3.33 % |
| Transition |
T>C |
All |
7589780 |
24.87 % |
| Transition |
C>T |
All |
1015151 |
3.33 % |
| Transversion |
A>C |
All |
307584 |
1.01 % |
| Transversion |
C>A |
All |
5178894 |
16.97 % |
| Transversion |
T>G |
All |
328106 |
1.08 % |
| Transversion |
G>T |
All |
5124015 |
16.79 % |
| Transversion |
A>T |
All |
814182 |
2.67 % |
| Transversion |
T>A |
All |
821193 |
2.69 % |
| Transversion |
C>G |
All |
302734 |
0.99 % |
| Transversion |
G>C |
All |
288315 |
0.94 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
290938 |
18.20 % |
| Transition |
G>A |
Passed |
221741 |
13.87 % |
| Transition |
T>C |
Passed |
289768 |
18.13 % |
| Transition |
C>T |
Passed |
226628 |
14.18 % |
| Transversion |
A>C |
Passed |
69707 |
4.36 % |
| Transversion |
C>A |
Passed |
78183 |
4.89 % |
| Transversion |
T>G |
Passed |
69835 |
4.37 % |
| Transversion |
G>T |
Passed |
78259 |
4.90 % |
| Transversion |
A>T |
Passed |
70904 |
4.44 % |
| Transversion |
T>A |
Passed |
70537 |
4.41 % |
| Transversion |
C>G |
Passed |
65919 |
4.12 % |
| Transversion |
G>C |
Passed |
65894 |
4.12 % |
| |
|
|
|
|
| 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 |
1.32 |
17356238 |
13165023 |
| Passed |
1.81 |
1029075 |
569238 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |