/EXTERNAL McGill EMC/variants/K006212_1_lane_gembs
BACK
SAMPLE K006212_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1132489553 |
246370969 |
21.75 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1132489553 |
100% |
1121817466 |
99.06 % |
10672087 |
0.94 % |
| |
|
|
|
|
|
|
| Passed |
249292570 |
22.01 % |
245162390 |
21.85 % |
4130180 |
1.66 % |
| Filtered |
883196983 |
77.99 % |
876655076 |
78.15 % |
6541907 |
2.62 % |
| |
|
|
|
|
|
|
| q20 |
845296792 |
95.71 % |
843083091 |
96.17 % |
2213701 |
33.84 % |
| q20,qd2 |
21932019 |
2.48 % |
17841112 |
2.04 % |
4090907 |
62.53 % |
| q20,mq40 |
11985706 |
1.36 % |
11918888 |
1.36 % |
66818 |
1.02 % |
| q20,qd2,mq40 |
3390139 |
0.38 % |
3331915 |
0.38 % |
58224 |
0.89 % |
| mq40 |
411105 |
0.05 % |
312032 |
0.04 % |
99073 |
1.51 % |
| qd2 |
158430 |
0.02 % |
150215 |
0.02 % |
8215 |
0.13 % |
| qd2,mq40 |
22244 |
0.00 % |
17823 |
0.00 % |
4421 |
0.07 % |
| qd2,fs60,mq40 |
287 |
0.00 % |
0 |
0.00 % |
287 |
0.00 % |
| fs60,mq40 |
134 |
0.00 % |
0 |
0.00 % |
134 |
0.00 % |
| qd2,fs60 |
81 |
0.00 % |
0 |
0.00 % |
81 |
0.00 % |
| q20,qd2,fs60,mq40 |
27 |
0.00 % |
0 |
0.00 % |
27 |
0.00 % |
| fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
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 |
2662907 |
21.33 % |
| Transition |
G>A |
All |
1472955 |
11.80 % |
| Transition |
T>C |
All |
2391423 |
19.15 % |
| Transition |
C>T |
All |
1494089 |
11.97 % |
| Transversion |
A>C |
All |
268279 |
2.15 % |
| Transversion |
C>A |
All |
1099291 |
8.80 % |
| Transversion |
T>G |
All |
307278 |
2.46 % |
| Transversion |
G>T |
All |
1068503 |
8.56 % |
| Transversion |
A>T |
All |
604043 |
4.84 % |
| Transversion |
T>A |
All |
628463 |
5.03 % |
| Transversion |
C>G |
All |
256250 |
2.05 % |
| Transversion |
G>C |
All |
233322 |
1.87 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
220078 |
15.08 % |
| Transition |
G>A |
Passed |
223060 |
15.28 % |
| Transition |
T>C |
Passed |
221546 |
15.18 % |
| Transition |
C>T |
Passed |
225574 |
15.45 % |
| Transversion |
A>C |
Passed |
70772 |
4.85 % |
| Transversion |
C>A |
Passed |
76980 |
5.27 % |
| Transversion |
T>G |
Passed |
70547 |
4.83 % |
| Transversion |
G>T |
Passed |
75814 |
5.19 % |
| Transversion |
A>T |
Passed |
66158 |
4.53 % |
| Transversion |
T>A |
Passed |
66367 |
4.55 % |
| Transversion |
C>G |
Passed |
71430 |
4.89 % |
| Transversion |
G>C |
Passed |
71432 |
4.89 % |
| |
|
|
|
|
| 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 |
1.80 |
8021374 |
4465429 |
| Passed |
1.56 |
890258 |
569500 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |