/EXTERNAL McGill EMC/variants/K006191_1_lane_gembs
BACK
SAMPLE K006191_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1137448127 |
112449348 |
9.89 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1137448127 |
100% |
1122442111 |
98.68 % |
15006016 |
1.32 % |
| |
|
|
|
|
|
|
| Passed |
118988113 |
10.46 % |
111411629 |
9.93 % |
7576484 |
6.37 % |
| Filtered |
1018460014 |
89.54 % |
1011030482 |
90.07 % |
7429532 |
6.24 % |
| |
|
|
|
|
|
|
| q20 |
975913746 |
95.82 % |
972953471 |
96.23 % |
2960275 |
39.84 % |
| q20,qd2 |
19834639 |
1.95 % |
15638852 |
1.55 % |
4195787 |
56.47 % |
| q20,mq40 |
17418583 |
1.71 % |
17342469 |
1.72 % |
76114 |
1.02 % |
| q20,qd2,mq40 |
4907894 |
0.48 % |
4844716 |
0.48 % |
63178 |
0.85 % |
| mq40 |
354595 |
0.03 % |
225470 |
0.02 % |
129125 |
1.74 % |
| qd2 |
18083 |
0.00 % |
15801 |
0.00 % |
2282 |
0.03 % |
| qd2,mq40 |
12256 |
0.00 % |
9703 |
0.00 % |
2553 |
0.03 % |
| qd2,fs60,mq40 |
93 |
0.00 % |
0 |
0.00 % |
93 |
0.00 % |
| fs60,mq40 |
62 |
0.00 % |
0 |
0.00 % |
62 |
0.00 % |
| qd2,fs60 |
29 |
0.00 % |
0 |
0.00 % |
29 |
0.00 % |
| fs60 |
17 |
0.00 % |
0 |
0.00 % |
17 |
0.00 % |
| q20,qd2,fs60,mq40 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| q20,qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
4396205 |
26.01 % |
| Transition |
G>A |
All |
1040902 |
6.16 % |
| Transition |
T>C |
All |
4265098 |
25.23 % |
| Transition |
C>T |
All |
1047518 |
6.20 % |
| Transversion |
A>C |
All |
295437 |
1.75 % |
| Transversion |
C>A |
All |
1277723 |
7.56 % |
| Transversion |
T>G |
All |
314412 |
1.86 % |
| Transversion |
G>T |
All |
1256426 |
7.43 % |
| Transversion |
A>T |
All |
1175836 |
6.96 % |
| Transversion |
T>A |
All |
1196450 |
7.08 % |
| Transversion |
C>G |
All |
323897 |
1.92 % |
| Transversion |
G>C |
All |
312400 |
1.85 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
160344 |
14.19 % |
| Transition |
G>A |
Passed |
152904 |
13.53 % |
| Transition |
T>C |
Passed |
162758 |
14.40 % |
| Transition |
C>T |
Passed |
155807 |
13.78 % |
| Transversion |
A>C |
Passed |
62106 |
5.49 % |
| Transversion |
C>A |
Passed |
65883 |
5.83 % |
| Transversion |
T>G |
Passed |
61623 |
5.45 % |
| Transversion |
G>T |
Passed |
66075 |
5.85 % |
| Transversion |
A>T |
Passed |
57457 |
5.08 % |
| Transversion |
T>A |
Passed |
57103 |
5.05 % |
| Transversion |
C>G |
Passed |
63822 |
5.65 % |
| Transversion |
G>C |
Passed |
64391 |
5.70 % |
| |
|
|
|
|
| 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 |
1.75 |
10749723 |
6152581 |
| Passed |
1.27 |
631813 |
498460 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |