/EXTERNAL McGill EMC/variants/K006137_1_lane_gembs
BACK
SAMPLE K006137_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1140143147 |
530923718 |
46.57 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1140143147 |
100% |
1127645356 |
98.90 % |
12497791 |
1.10 % |
| |
|
|
|
|
|
|
| Passed |
533157970 |
46.76 % |
529167365 |
46.93 % |
3990605 |
0.75 % |
| Filtered |
606985177 |
53.24 % |
598477991 |
53.07 % |
8507186 |
1.60 % |
| |
|
|
|
|
|
|
| q20 |
567040045 |
93.42 % |
564839372 |
94.38 % |
2200673 |
25.87 % |
| q20,qd2 |
20276350 |
3.34 % |
14318810 |
2.39 % |
5957540 |
70.03 % |
| q20,mq40 |
13864608 |
2.28 % |
13765365 |
2.30 % |
99243 |
1.17 % |
| q20,qd2,mq40 |
3973744 |
0.65 % |
3886870 |
0.65 % |
86874 |
1.02 % |
| qd2 |
990191 |
0.16 % |
959838 |
0.16 % |
30353 |
0.36 % |
| mq40 |
815438 |
0.13 % |
688211 |
0.11 % |
127227 |
1.50 % |
| qd2,mq40 |
24224 |
0.00 % |
19525 |
0.00 % |
4699 |
0.06 % |
| qd2,fs60,mq40 |
312 |
0.00 % |
0 |
0.00 % |
312 |
0.00 % |
| fs60,mq40 |
115 |
0.00 % |
0 |
0.00 % |
115 |
0.00 % |
| qd2,fs60 |
104 |
0.00 % |
0 |
0.00 % |
104 |
0.00 % |
| q20,qd2,fs60,mq40 |
25 |
0.00 % |
0 |
0.00 % |
25 |
0.00 % |
| fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
3904259 |
27.41 % |
| Transition |
G>A |
All |
1348476 |
9.47 % |
| Transition |
T>C |
All |
3463811 |
24.32 % |
| Transition |
C>T |
All |
1383664 |
9.72 % |
| Transversion |
A>C |
All |
333975 |
2.34 % |
| Transversion |
C>A |
All |
949394 |
6.67 % |
| Transversion |
T>G |
All |
365480 |
2.57 % |
| Transversion |
G>T |
All |
913099 |
6.41 % |
| Transversion |
A>T |
All |
467778 |
3.28 % |
| Transversion |
T>A |
All |
500341 |
3.51 % |
| Transversion |
C>G |
All |
318520 |
2.24 % |
| Transversion |
G>C |
All |
293617 |
2.06 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
397835 |
16.81 % |
| Transition |
G>A |
Passed |
363943 |
15.38 % |
| Transition |
T>C |
Passed |
400249 |
16.91 % |
| Transition |
C>T |
Passed |
369235 |
15.60 % |
| Transversion |
A>C |
Passed |
104233 |
4.40 % |
| Transversion |
C>A |
Passed |
111239 |
4.70 % |
| Transversion |
T>G |
Passed |
104179 |
4.40 % |
| Transversion |
G>T |
Passed |
111645 |
4.72 % |
| Transversion |
A>T |
Passed |
100220 |
4.23 % |
| Transversion |
T>A |
Passed |
100004 |
4.23 % |
| Transversion |
C>G |
Passed |
102107 |
4.31 % |
| Transversion |
G>C |
Passed |
101735 |
4.30 % |
| |
|
|
|
|
| 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 |
2.44 |
10100210 |
4142204 |
| Passed |
1.83 |
1531262 |
835362 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |