/EXTERNAL McGill EMC/variants/K006166_1_lane_gembs
BACK
SAMPLE K006166_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1130039700 |
263584426 |
23.33 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1130039700 |
100% |
1118926836 |
99.02 % |
11112864 |
0.98 % |
| |
|
|
|
|
|
|
| Passed |
266143380 |
23.55 % |
262354415 |
23.45 % |
3788965 |
1.42 % |
| Filtered |
863896320 |
76.45 % |
856572421 |
76.55 % |
7323899 |
2.75 % |
| |
|
|
|
|
|
|
| q20 |
819057712 |
94.81 % |
816704885 |
95.35 % |
2352827 |
32.13 % |
| q20,qd2 |
26360623 |
3.05 % |
21630083 |
2.53 % |
4730540 |
64.59 % |
| q20,mq40 |
13792876 |
1.60 % |
13716664 |
1.60 % |
76212 |
1.04 % |
| q20,qd2,mq40 |
4135257 |
0.48 % |
4076129 |
0.48 % |
59128 |
0.81 % |
| mq40 |
377453 |
0.04 % |
283995 |
0.03 % |
93458 |
1.28 % |
| qd2 |
152763 |
0.02 % |
145163 |
0.02 % |
7600 |
0.10 % |
| qd2,mq40 |
19204 |
0.00 % |
15502 |
0.00 % |
3702 |
0.05 % |
| qd2,fs60,mq40 |
206 |
0.00 % |
0 |
0.00 % |
206 |
0.00 % |
| fs60,mq40 |
121 |
0.00 % |
0 |
0.00 % |
121 |
0.00 % |
| qd2,fs60 |
71 |
0.00 % |
0 |
0.00 % |
71 |
0.00 % |
| q20,qd2,fs60,mq40 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
2621156 |
20.28 % |
| Transition |
G>A |
All |
1252926 |
9.69 % |
| Transition |
T>C |
All |
2518663 |
19.49 % |
| Transition |
C>T |
All |
1261856 |
9.76 % |
| Transversion |
A>C |
All |
346759 |
2.68 % |
| Transversion |
C>A |
All |
1418070 |
10.97 % |
| Transversion |
T>G |
All |
359860 |
2.78 % |
| Transversion |
G>T |
All |
1390598 |
10.76 % |
| Transversion |
A>T |
All |
582682 |
4.51 % |
| Transversion |
T>A |
All |
590472 |
4.57 % |
| Transversion |
C>G |
All |
295421 |
2.29 % |
| Transversion |
G>C |
All |
286482 |
2.22 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
235069 |
15.48 % |
| Transition |
G>A |
Passed |
225153 |
14.82 % |
| Transition |
T>C |
Passed |
238320 |
15.69 % |
| Transition |
C>T |
Passed |
228112 |
15.02 % |
| Transversion |
A>C |
Passed |
74052 |
4.88 % |
| Transversion |
C>A |
Passed |
79211 |
5.22 % |
| Transversion |
T>G |
Passed |
74119 |
4.88 % |
| Transversion |
G>T |
Passed |
78645 |
5.18 % |
| Transversion |
A>T |
Passed |
70330 |
4.63 % |
| Transversion |
T>A |
Passed |
70533 |
4.64 % |
| Transversion |
C>G |
Passed |
72596 |
4.78 % |
| Transversion |
G>C |
Passed |
72653 |
4.78 % |
| |
|
|
|
|
| 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 |
1.45 |
7654601 |
5270344 |
| Passed |
1.56 |
926654 |
592139 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |