/EXTERNAL McGill EMC/variants/K006207_1_lane_gembs
BACK
SAMPLE K006207_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1138099341 |
132901626 |
11.68 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1138099341 |
100% |
1123177928 |
98.69 % |
14921413 |
1.31 % |
| |
|
|
|
|
|
|
| Passed |
137341504 |
12.07 % |
131807924 |
11.74 % |
5533580 |
4.03 % |
| Filtered |
1000757837 |
87.93 % |
991370004 |
88.26 % |
9387833 |
6.84 % |
| |
|
|
|
|
|
|
| q20 |
947677125 |
94.70 % |
944140214 |
95.24 % |
3536911 |
37.68 % |
| q20,qd2 |
30148194 |
3.01 % |
24600741 |
2.48 % |
5547453 |
59.09 % |
| q20,mq40 |
16752564 |
1.67 % |
16649785 |
1.68 % |
102779 |
1.09 % |
| q20,qd2,mq40 |
5852960 |
0.58 % |
5768397 |
0.58 % |
84563 |
0.90 % |
| mq40 |
283586 |
0.03 % |
173277 |
0.02 % |
110309 |
1.18 % |
| qd2 |
28915 |
0.00 % |
26182 |
0.00 % |
2733 |
0.03 % |
| qd2,mq40 |
14261 |
0.00 % |
11408 |
0.00 % |
2853 |
0.03 % |
| qd2,fs60,mq40 |
106 |
0.00 % |
0 |
0.00 % |
106 |
0.00 % |
| fs60,mq40 |
62 |
0.00 % |
0 |
0.00 % |
62 |
0.00 % |
| qd2,fs60 |
47 |
0.00 % |
0 |
0.00 % |
47 |
0.00 % |
| q20,qd2,fs60,mq40 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
4084008 |
24.21 % |
| Transition |
G>A |
All |
1138725 |
6.75 % |
| Transition |
T>C |
All |
3764835 |
22.31 % |
| Transition |
C>T |
All |
1144161 |
6.78 % |
| Transversion |
A>C |
All |
297082 |
1.76 % |
| Transversion |
C>A |
All |
1853987 |
10.99 % |
| Transversion |
T>G |
All |
346867 |
2.06 % |
| Transversion |
G>T |
All |
1778720 |
10.54 % |
| Transversion |
A>T |
All |
922746 |
5.47 % |
| Transversion |
T>A |
All |
973220 |
5.77 % |
| Transversion |
C>G |
All |
299910 |
1.78 % |
| Transversion |
G>C |
All |
268300 |
1.59 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
179866 |
14.67 % |
| Transition |
G>A |
Passed |
167897 |
13.69 % |
| Transition |
T>C |
Passed |
189086 |
15.42 % |
| Transition |
C>T |
Passed |
172895 |
14.10 % |
| Transversion |
A>C |
Passed |
63491 |
5.18 % |
| Transversion |
C>A |
Passed |
69345 |
5.66 % |
| Transversion |
T>G |
Passed |
63892 |
5.21 % |
| Transversion |
G>T |
Passed |
69067 |
5.63 % |
| Transversion |
A>T |
Passed |
62123 |
5.07 % |
| Transversion |
T>A |
Passed |
61097 |
4.98 % |
| Transversion |
C>G |
Passed |
63968 |
5.22 % |
| Transversion |
G>C |
Passed |
63406 |
5.17 % |
| |
|
|
|
|
| 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 |
1.50 |
10131729 |
6740832 |
| Passed |
1.37 |
709744 |
516389 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |