/EXTERNAL McGill EMC/variants/K006146_1_lane_gembs
BACK
SAMPLE K006146_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1161724425 |
428061429 |
36.85 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1161724425 |
100% |
1141606129 |
98.27 % |
20118296 |
1.73 % |
| |
|
|
|
|
|
|
| Passed |
432457896 |
37.23 % |
426084599 |
37.32 % |
6373297 |
1.47 % |
| Filtered |
729266529 |
62.77 % |
715521530 |
62.68 % |
13744999 |
3.18 % |
| |
|
|
|
|
|
|
| q20 |
699007195 |
95.85 % |
694296405 |
97.03 % |
4710790 |
34.27 % |
| q20,qd2 |
17975533 |
2.46 % |
9200422 |
1.29 % |
8775111 |
63.84 % |
| q20,mq40 |
8634806 |
1.18 % |
8565491 |
1.20 % |
69315 |
0.50 % |
| q20,qd2,mq40 |
3018777 |
0.41 % |
2957509 |
0.41 % |
61268 |
0.45 % |
| mq40 |
449046 |
0.06 % |
342951 |
0.05 % |
106095 |
0.77 % |
| qd2 |
158863 |
0.02 % |
141963 |
0.02 % |
16900 |
0.12 % |
| qd2,mq40 |
21723 |
0.00 % |
16789 |
0.00 % |
4934 |
0.04 % |
| qd2,fs60,mq40 |
243 |
0.00 % |
0 |
0.00 % |
243 |
0.00 % |
| qd2,fs60 |
171 |
0.00 % |
0 |
0.00 % |
171 |
0.00 % |
| fs60,mq40 |
109 |
0.00 % |
0 |
0.00 % |
109 |
0.00 % |
| fs60 |
31 |
0.00 % |
0 |
0.00 % |
31 |
0.00 % |
| q20,qd2,fs60,mq40 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| q20,qd2,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
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 |
7620375 |
34.74 % |
| Transition |
G>A |
All |
1137829 |
5.19 % |
| Transition |
T>C |
All |
5832343 |
26.59 % |
| Transition |
C>T |
All |
1250718 |
5.70 % |
| Transversion |
A>C |
All |
347090 |
1.58 % |
| Transversion |
C>A |
All |
1181509 |
5.39 % |
| Transversion |
T>G |
All |
503464 |
2.30 % |
| Transversion |
G>T |
All |
1078996 |
4.92 % |
| Transversion |
A>T |
All |
1035653 |
4.72 % |
| Transversion |
T>A |
All |
1162023 |
5.30 % |
| Transversion |
C>G |
All |
444882 |
2.03 % |
| Transversion |
G>C |
All |
340540 |
1.55 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
445581 |
18.35 % |
| Transition |
G>A |
Passed |
334978 |
13.79 % |
| Transition |
T>C |
Passed |
417263 |
17.18 % |
| Transition |
C>T |
Passed |
340578 |
14.02 % |
| Transversion |
A>C |
Passed |
115234 |
4.74 % |
| Transversion |
C>A |
Passed |
111733 |
4.60 % |
| Transversion |
T>G |
Passed |
117075 |
4.82 % |
| Transversion |
G>T |
Passed |
113530 |
4.67 % |
| Transversion |
A>T |
Passed |
101702 |
4.19 % |
| Transversion |
T>A |
Passed |
100920 |
4.16 % |
| Transversion |
C>G |
Passed |
115384 |
4.75 % |
| Transversion |
G>C |
Passed |
114753 |
4.72 % |
| |
|
|
|
|
| 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 |
2.60 |
15841265 |
6094157 |
| Passed |
1.73 |
1538400 |
890331 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |