/EXTERNAL McGill EMC/variants/K006178_1_lane_gembs
BACK
SAMPLE K006178_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1154807239 |
782951472 |
67.80 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1154807239 |
100% |
1140452665 |
98.76 % |
14354574 |
1.24 % |
| |
|
|
|
|
|
|
| Passed |
784907134 |
67.97 % |
780858911 |
68.47 % |
4048223 |
0.52 % |
| Filtered |
369900105 |
32.03 % |
359593754 |
31.53 % |
10306351 |
1.31 % |
| |
|
|
|
|
|
|
| q20 |
336855696 |
91.07 % |
334832359 |
93.11 % |
2023337 |
19.63 % |
| q20,qd2 |
15021464 |
4.06 % |
7103947 |
1.98 % |
7917517 |
76.82 % |
| q20,mq40 |
12549743 |
3.39 % |
12461857 |
3.47 % |
87886 |
0.85 % |
| q20,qd2,mq40 |
3438249 |
0.93 % |
3342510 |
0.93 % |
95739 |
0.93 % |
| mq40 |
1187994 |
0.32 % |
1047489 |
0.29 % |
140505 |
1.36 % |
| qd2 |
817445 |
0.22 % |
782122 |
0.22 % |
35323 |
0.34 % |
| qd2,mq40 |
28919 |
0.01 % |
23470 |
0.01 % |
5449 |
0.05 % |
| qd2,fs60,mq40 |
285 |
0.00 % |
0 |
0.00 % |
285 |
0.00 % |
| fs60,mq40 |
133 |
0.00 % |
0 |
0.00 % |
133 |
0.00 % |
| qd2,fs60 |
110 |
0.00 % |
0 |
0.00 % |
110 |
0.00 % |
| q20,qd2,fs60,mq40 |
38 |
0.00 % |
0 |
0.00 % |
38 |
0.00 % |
| fs60 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| q20,qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
5271381 |
32.85 % |
| Transition |
G>A |
All |
1229296 |
7.66 % |
| Transition |
T>C |
All |
4941400 |
30.79 % |
| Transition |
C>T |
All |
1247733 |
7.78 % |
| Transversion |
A>C |
All |
236158 |
1.47 % |
| Transversion |
C>A |
All |
766997 |
4.78 % |
| Transversion |
T>G |
All |
251559 |
1.57 % |
| Transversion |
G>T |
All |
731321 |
4.56 % |
| Transversion |
A>T |
All |
439225 |
2.74 % |
| Transversion |
T>A |
All |
451243 |
2.81 % |
| Transversion |
C>G |
All |
245059 |
1.53 % |
| Transversion |
G>C |
All |
235541 |
1.47 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
508254 |
17.20 % |
| Transition |
G>A |
Passed |
469402 |
15.89 % |
| Transition |
T>C |
Passed |
511813 |
17.32 % |
| Transition |
C>T |
Passed |
476961 |
16.14 % |
| Transversion |
A>C |
Passed |
124176 |
4.20 % |
| Transversion |
C>A |
Passed |
129578 |
4.39 % |
| Transversion |
T>G |
Passed |
124560 |
4.22 % |
| Transversion |
G>T |
Passed |
129639 |
4.39 % |
| Transversion |
A>T |
Passed |
111307 |
3.77 % |
| Transversion |
T>A |
Passed |
111505 |
3.77 % |
| Transversion |
C>G |
Passed |
128743 |
4.36 % |
| Transversion |
G>C |
Passed |
128628 |
4.35 % |
| |
|
|
|
|
| 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 |
3.78 |
12689810 |
3357103 |
| Passed |
1.99 |
1966430 |
988136 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |