/EXTERNAL McGill EMC/variants/K006180_1_lane_gembs
BACK
SAMPLE K006180_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1145690667 |
846137629 |
73.85 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1145690667 |
100% |
1136727588 |
99.22 % |
8963079 |
0.78 % |
| |
|
|
|
|
|
|
| Passed |
847134806 |
73.94 % |
843975479 |
74.25 % |
3159327 |
0.37 % |
| Filtered |
298555861 |
26.06 % |
292752109 |
25.75 % |
5803752 |
0.69 % |
| |
|
|
|
|
|
|
| q20 |
267971487 |
89.76 % |
266910785 |
91.17 % |
1060702 |
18.28 % |
| q20,qd2 |
11339940 |
3.80 % |
6981361 |
2.38 % |
4358579 |
75.10 % |
| q20,mq40 |
11233657 |
3.76 % |
11147987 |
3.81 % |
85670 |
1.48 % |
| qd2 |
3310007 |
1.11 % |
3258855 |
1.11 % |
51152 |
0.88 % |
| q20,qd2,mq40 |
2650067 |
0.89 % |
2547851 |
0.87 % |
102216 |
1.76 % |
| mq40 |
2004087 |
0.67 % |
1868193 |
0.64 % |
135894 |
2.34 % |
| qd2,mq40 |
45188 |
0.02 % |
37077 |
0.01 % |
8111 |
0.14 % |
| qd2,fs60,mq40 |
657 |
0.00 % |
0 |
0.00 % |
657 |
0.01 % |
| fs60,mq40 |
277 |
0.00 % |
0 |
0.00 % |
277 |
0.00 % |
| qd2,fs60 |
236 |
0.00 % |
0 |
0.00 % |
236 |
0.00 % |
| fs60 |
153 |
0.00 % |
0 |
0.00 % |
153 |
0.00 % |
| q20,qd2,fs60,mq40 |
65 |
0.00 % |
0 |
0.00 % |
65 |
0.00 % |
| q20,qd2,fs60 |
40 |
0.00 % |
0 |
0.00 % |
40 |
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 |
2828070 |
26.62 % |
| Transition |
G>A |
All |
1021990 |
9.62 % |
| Transition |
T>C |
All |
2729743 |
25.69 % |
| Transition |
C>T |
All |
1030799 |
9.70 % |
| Transversion |
A>C |
All |
210270 |
1.98 % |
| Transversion |
C>A |
All |
770432 |
7.25 % |
| Transversion |
T>G |
All |
214248 |
2.02 % |
| Transversion |
G>T |
All |
773992 |
7.29 % |
| Transversion |
A>T |
All |
304926 |
2.87 % |
| Transversion |
T>A |
All |
302764 |
2.85 % |
| Transversion |
C>G |
All |
219378 |
2.06 % |
| Transversion |
G>C |
All |
217050 |
2.04 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
522911 |
16.75 % |
| Transition |
G>A |
Passed |
509194 |
16.31 % |
| Transition |
T>C |
Passed |
525026 |
16.82 % |
| Transition |
C>T |
Passed |
513178 |
16.44 % |
| Transversion |
A>C |
Passed |
131830 |
4.22 % |
| Transversion |
C>A |
Passed |
140487 |
4.50 % |
| Transversion |
T>G |
Passed |
131270 |
4.21 % |
| Transversion |
G>T |
Passed |
137854 |
4.42 % |
| Transversion |
A>T |
Passed |
118718 |
3.80 % |
| Transversion |
T>A |
Passed |
118835 |
3.81 % |
| Transversion |
C>G |
Passed |
135940 |
4.36 % |
| Transversion |
G>C |
Passed |
136172 |
4.36 % |
| |
|
|
|
|
| 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 |
2.53 |
7610602 |
3013060 |
| Passed |
1.97 |
2070309 |
1051106 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |