/EXTERNAL McGill EMC/variants/K006129_1_lane_gembs
BACK
SAMPLE K006129_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1075471917 |
56324974 |
5.24 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1075471917 |
100% |
1063906542 |
98.92 % |
11565375 |
1.08 % |
| |
|
|
|
|
|
|
| Passed |
59404053 |
5.52 % |
55710738 |
5.24 % |
3693315 |
6.22 % |
| Filtered |
1016067864 |
94.48 % |
1008195804 |
94.76 % |
7872060 |
13.25 % |
| |
|
|
|
|
|
|
| q20 |
906592534 |
89.23 % |
902993760 |
89.57 % |
3598774 |
45.72 % |
| q20,qd2 |
84462917 |
8.31 % |
80409605 |
7.98 % |
4053312 |
51.49 % |
| q20,mq40 |
17417855 |
1.71 % |
17328282 |
1.72 % |
89573 |
1.14 % |
| q20,qd2,mq40 |
7388957 |
0.73 % |
7340289 |
0.73 % |
48668 |
0.62 % |
| mq40 |
172826 |
0.02 % |
95093 |
0.01 % |
77733 |
0.99 % |
| qd2 |
22366 |
0.00 % |
20589 |
0.00 % |
1777 |
0.02 % |
| qd2,mq40 |
10192 |
0.00 % |
8186 |
0.00 % |
2006 |
0.03 % |
| qd2,fs60,mq40 |
106 |
0.00 % |
0 |
0.00 % |
106 |
0.00 % |
| qd2,fs60 |
50 |
0.00 % |
0 |
0.00 % |
50 |
0.00 % |
| fs60,mq40 |
49 |
0.00 % |
0 |
0.00 % |
49 |
0.00 % |
| fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
2445638 |
17.74 % |
| Transition |
G>A |
All |
1054733 |
7.65 % |
| Transition |
T>C |
All |
2300228 |
16.69 % |
| Transition |
C>T |
All |
1066151 |
7.74 % |
| Transversion |
A>C |
All |
596552 |
4.33 % |
| Transversion |
C>A |
All |
1617304 |
11.73 % |
| Transversion |
T>G |
All |
611239 |
4.43 % |
| Transversion |
G>T |
All |
1586066 |
11.51 % |
| Transversion |
A>T |
All |
815789 |
5.92 % |
| Transversion |
T>A |
All |
840045 |
6.09 % |
| Transversion |
C>G |
All |
427078 |
3.10 % |
| Transversion |
G>C |
All |
421916 |
3.06 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
106071 |
15.74 % |
| Transition |
G>A |
Passed |
83279 |
12.36 % |
| Transition |
T>C |
Passed |
113738 |
16.88 % |
| Transition |
C>T |
Passed |
85432 |
12.68 % |
| Transversion |
A>C |
Passed |
36186 |
5.37 % |
| Transversion |
C>A |
Passed |
37633 |
5.59 % |
| Transversion |
T>G |
Passed |
36083 |
5.36 % |
| Transversion |
G>T |
Passed |
37465 |
5.56 % |
| Transversion |
A>T |
Passed |
36162 |
5.37 % |
| Transversion |
T>A |
Passed |
36127 |
5.36 % |
| Transversion |
C>G |
Passed |
32977 |
4.89 % |
| Transversion |
G>C |
Passed |
32638 |
4.84 % |
| |
|
|
|
|
| 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 |
0.99 |
6866750 |
6915989 |
| Passed |
1.36 |
388520 |
285271 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |