/EXTERNAL McGill EMC/variants/K006160_1_lane_gembs
BACK
SAMPLE K006160_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1173354145 |
532038560 |
45.34 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1173354145 |
100% |
1128265198 |
96.16 % |
45088947 |
3.84 % |
| |
|
|
|
|
|
|
| Passed |
542581168 |
46.24 % |
527584460 |
46.76 % |
14996708 |
2.76 % |
| Filtered |
630772977 |
53.76 % |
600680738 |
53.24 % |
30092239 |
5.55 % |
| |
|
|
|
|
|
|
| q20 |
564498226 |
89.49 % |
557891752 |
92.88 % |
6606474 |
21.95 % |
| q20,qd2 |
33213988 |
5.27 % |
13047325 |
2.17 % |
20166663 |
67.02 % |
| q20,mq40 |
21168321 |
3.36 % |
20603882 |
3.43 % |
564439 |
1.88 % |
| mq40 |
5980261 |
0.95 % |
4357591 |
0.73 % |
1622670 |
5.39 % |
| q20,qd2,mq40 |
5276878 |
0.84 % |
4254342 |
0.71 % |
1022536 |
3.40 % |
| qd2 |
590657 |
0.09 % |
493044 |
0.08 % |
97613 |
0.32 % |
| qd2,mq40 |
44207 |
0.01 % |
32802 |
0.01 % |
11405 |
0.04 % |
| qd2,fs60,mq40 |
238 |
0.00 % |
0 |
0.00 % |
238 |
0.00 % |
| fs60,mq40 |
122 |
0.00 % |
0 |
0.00 % |
122 |
0.00 % |
| qd2,fs60 |
48 |
0.00 % |
0 |
0.00 % |
48 |
0.00 % |
| q20,qd2,fs60,mq40 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| q20,qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
13006963 |
27.65 % |
| Transition |
G>A |
All |
3981341 |
8.46 % |
| Transition |
T>C |
All |
12792687 |
27.19 % |
| Transition |
C>T |
All |
3791557 |
8.06 % |
| Transversion |
A>C |
All |
763429 |
1.62 % |
| Transversion |
C>A |
All |
3520646 |
7.48 % |
| Transversion |
T>G |
All |
779997 |
1.66 % |
| Transversion |
G>T |
All |
3516207 |
7.47 % |
| Transversion |
A>T |
All |
1670236 |
3.55 % |
| Transversion |
T>A |
All |
1636973 |
3.48 % |
| Transversion |
C>G |
All |
800845 |
1.70 % |
| Transversion |
G>C |
All |
784544 |
1.67 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1087466 |
21.93 % |
| Transition |
G>A |
Passed |
629997 |
12.70 % |
| Transition |
T>C |
Passed |
1052700 |
21.22 % |
| Transition |
C>T |
Passed |
602544 |
12.15 % |
| Transversion |
A>C |
Passed |
204448 |
4.12 % |
| Transversion |
C>A |
Passed |
191592 |
3.86 % |
| Transversion |
T>G |
Passed |
207944 |
4.19 % |
| Transversion |
G>T |
Passed |
187683 |
3.78 % |
| Transversion |
A>T |
Passed |
170752 |
3.44 % |
| Transversion |
T>A |
Passed |
173272 |
3.49 % |
| Transversion |
C>G |
Passed |
227866 |
4.59 % |
| Transversion |
G>C |
Passed |
223664 |
4.51 % |
| |
|
|
|
|
| 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 |
2.49 |
33572548 |
13472877 |
| Passed |
2.12 |
3372707 |
1587221 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |