/EXTERNAL McGill EMC/variants/K006127_1_lane_gembs
BACK
SAMPLE K006127_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1152259950 |
869000945 |
75.42 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1152259950 |
100% |
1134939382 |
98.50 % |
17320568 |
1.50 % |
| |
|
|
|
|
|
|
| Passed |
870657879 |
75.56 % |
865654703 |
76.27 % |
5003176 |
0.57 % |
| Filtered |
281602071 |
24.44 % |
269284679 |
23.73 % |
12317392 |
1.41 % |
| |
|
|
|
|
|
|
| q20 |
246984127 |
87.71 % |
244857699 |
90.93 % |
2126428 |
17.26 % |
| q20,qd2 |
15851444 |
5.63 % |
6088446 |
2.26 % |
9762998 |
79.26 % |
| q20,mq40 |
13169244 |
4.68 % |
13065159 |
4.85 % |
104085 |
0.85 % |
| q20,qd2,mq40 |
3638009 |
1.29 % |
3534314 |
1.31 % |
103695 |
0.84 % |
| mq40 |
1165122 |
0.41 % |
1005605 |
0.37 % |
159517 |
1.30 % |
| qd2 |
765170 |
0.27 % |
711048 |
0.26 % |
54122 |
0.44 % |
| qd2,mq40 |
28318 |
0.01 % |
22408 |
0.01 % |
5910 |
0.05 % |
| qd2,fs60,mq40 |
358 |
0.00 % |
0 |
0.00 % |
358 |
0.00 % |
| fs60,mq40 |
142 |
0.00 % |
0 |
0.00 % |
142 |
0.00 % |
| qd2,fs60 |
89 |
0.00 % |
0 |
0.00 % |
89 |
0.00 % |
| q20,qd2,fs60,mq40 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
6340618 |
34.36 % |
| Transition |
G>A |
All |
1321155 |
7.16 % |
| Transition |
T>C |
All |
6278526 |
34.03 % |
| Transition |
C>T |
All |
1322467 |
7.17 % |
| Transversion |
A>C |
All |
264060 |
1.43 % |
| Transversion |
C>A |
All |
573551 |
3.11 % |
| Transversion |
T>G |
All |
268060 |
1.45 % |
| Transversion |
G>T |
All |
568439 |
3.08 % |
| Transversion |
A>T |
All |
488418 |
2.65 % |
| Transversion |
T>A |
All |
484028 |
2.62 % |
| Transversion |
C>G |
All |
272461 |
1.48 % |
| Transversion |
G>C |
All |
269762 |
1.46 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
655213 |
16.66 % |
| Transition |
G>A |
Passed |
617141 |
15.69 % |
| Transition |
T>C |
Passed |
656152 |
16.68 % |
| Transition |
C>T |
Passed |
618888 |
15.74 % |
| Transversion |
A>C |
Passed |
173228 |
4.40 % |
| Transversion |
C>A |
Passed |
180334 |
4.59 % |
| Transversion |
T>G |
Passed |
173896 |
4.42 % |
| Transversion |
G>T |
Passed |
180943 |
4.60 % |
| Transversion |
A>T |
Passed |
160432 |
4.08 % |
| Transversion |
T>A |
Passed |
160787 |
4.09 % |
| Transversion |
C>G |
Passed |
177853 |
4.52 % |
| Transversion |
G>C |
Passed |
178008 |
4.53 % |
| |
|
|
|
|
| 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 |
4.79 |
15262766 |
3188779 |
| Passed |
1.84 |
2547394 |
1385481 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |