/EXTERNAL McGill EMC/variants/K006192_1_lane_gembs
BACK
SAMPLE K006192_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1131265754 |
252706282 |
22.34 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1131265754 |
100% |
1121069675 |
99.10 % |
10196079 |
0.90 % |
| |
|
|
|
|
|
|
| Passed |
255576085 |
22.59 % |
251472184 |
22.43 % |
4103901 |
1.61 % |
| Filtered |
875689669 |
77.41 % |
869597491 |
77.57 % |
6092178 |
2.38 % |
| |
|
|
|
|
|
|
| q20 |
836483317 |
95.52 % |
834435665 |
95.96 % |
2047652 |
33.61 % |
| q20,qd2 |
23109614 |
2.64 % |
19276256 |
2.22 % |
3833358 |
62.92 % |
| q20,mq40 |
12087730 |
1.38 % |
12026748 |
1.38 % |
60982 |
1.00 % |
| q20,qd2,mq40 |
3535953 |
0.40 % |
3484498 |
0.40 % |
51455 |
0.84 % |
| mq40 |
338778 |
0.04 % |
251974 |
0.03 % |
86804 |
1.42 % |
| qd2 |
114582 |
0.01 % |
106830 |
0.01 % |
7752 |
0.13 % |
| qd2,mq40 |
19279 |
0.00 % |
15520 |
0.00 % |
3759 |
0.06 % |
| qd2,fs60,mq40 |
208 |
0.00 % |
0 |
0.00 % |
208 |
0.00 % |
| fs60,mq40 |
118 |
0.00 % |
0 |
0.00 % |
118 |
0.00 % |
| qd2,fs60 |
58 |
0.00 % |
0 |
0.00 % |
58 |
0.00 % |
| q20,qd2,fs60,mq40 |
20 |
0.00 % |
0 |
0.00 % |
20 |
0.00 % |
| fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
2653257 |
22.15 % |
| Transition |
G>A |
All |
1280463 |
10.69 % |
| Transition |
T>C |
All |
2596073 |
21.67 % |
| Transition |
C>T |
All |
1280617 |
10.69 % |
| Transversion |
A>C |
All |
289847 |
2.42 % |
| Transversion |
C>A |
All |
943857 |
7.88 % |
| Transversion |
T>G |
All |
299183 |
2.50 % |
| Transversion |
G>T |
All |
922146 |
7.70 % |
| Transversion |
A>T |
All |
594718 |
4.97 % |
| Transversion |
T>A |
All |
598313 |
5.00 % |
| Transversion |
C>G |
All |
262710 |
2.19 % |
| Transversion |
G>C |
All |
256891 |
2.14 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
230143 |
15.32 % |
| Transition |
G>A |
Passed |
223424 |
14.87 % |
| Transition |
T>C |
Passed |
233286 |
15.52 % |
| Transition |
C>T |
Passed |
226880 |
15.10 % |
| Transversion |
A>C |
Passed |
73753 |
4.91 % |
| Transversion |
C>A |
Passed |
77987 |
5.19 % |
| Transversion |
T>G |
Passed |
74045 |
4.93 % |
| Transversion |
G>T |
Passed |
77755 |
5.17 % |
| Transversion |
A>T |
Passed |
69497 |
4.62 % |
| Transversion |
T>A |
Passed |
69607 |
4.63 % |
| Transversion |
C>G |
Passed |
73035 |
4.86 % |
| Transversion |
G>C |
Passed |
73257 |
4.88 % |
| |
|
|
|
|
| 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 |
1.87 |
7810410 |
4167665 |
| Passed |
1.55 |
913733 |
588936 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |