/EXTERNAL McGill EMC/variants/K006152_1_lane_gembs
BACK
SAMPLE K006152_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1145043313 |
574527348 |
50.18 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1145043313 |
100% |
1130181022 |
98.70 % |
14862291 |
1.30 % |
| |
|
|
|
|
|
|
| Passed |
576784564 |
50.37 % |
572900423 |
50.69 % |
3884141 |
0.67 % |
| Filtered |
568258749 |
49.63 % |
557280599 |
49.31 % |
10978150 |
1.90 % |
| |
|
|
|
|
|
|
| q20 |
523719351 |
92.16 % |
521157545 |
93.52 % |
2561806 |
23.34 % |
| q20,qd2 |
20011404 |
3.52 % |
12083749 |
2.17 % |
7927655 |
72.21 % |
| q20,mq40 |
13105579 |
2.31 % |
13007890 |
2.33 % |
97689 |
0.89 % |
| qd2 |
5541595 |
0.98 % |
5470532 |
0.98 % |
71063 |
0.65 % |
| mq40 |
3301925 |
0.58 % |
3151848 |
0.57 % |
150077 |
1.37 % |
| q20,qd2,mq40 |
2506723 |
0.44 % |
2352254 |
0.42 % |
154469 |
1.41 % |
| qd2,mq40 |
66909 |
0.01 % |
56781 |
0.01 % |
10128 |
0.09 % |
| qd2,fs60 |
1458 |
0.00 % |
0 |
0.00 % |
1458 |
0.01 % |
| qd2,fs60,mq40 |
1288 |
0.00 % |
0 |
0.00 % |
1288 |
0.01 % |
| fs60 |
1138 |
0.00 % |
0 |
0.00 % |
1138 |
0.01 % |
| q20,qd2,fs60 |
662 |
0.00 % |
0 |
0.00 % |
662 |
0.01 % |
| fs60,mq40 |
487 |
0.00 % |
0 |
0.00 % |
487 |
0.00 % |
| q20,qd2,fs60,mq40 |
228 |
0.00 % |
0 |
0.00 % |
228 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
4102363 |
24.28 % |
| Transition |
G>A |
All |
1593088 |
9.43 % |
| Transition |
T>C |
All |
3298192 |
19.52 % |
| Transition |
C>T |
All |
1601366 |
9.48 % |
| Transversion |
A>C |
All |
261388 |
1.55 % |
| Transversion |
C>A |
All |
2113387 |
12.51 % |
| Transversion |
T>G |
All |
326892 |
1.94 % |
| Transversion |
G>T |
All |
2078628 |
12.30 % |
| Transversion |
A>T |
All |
449349 |
2.66 % |
| Transversion |
T>A |
All |
503558 |
2.98 % |
| Transversion |
C>G |
All |
299637 |
1.77 % |
| Transversion |
G>C |
All |
264804 |
1.57 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
373942 |
16.86 % |
| Transition |
G>A |
Passed |
356411 |
16.07 % |
| Transition |
T>C |
Passed |
373211 |
16.83 % |
| Transition |
C>T |
Passed |
363217 |
16.38 % |
| Transversion |
A>C |
Passed |
93836 |
4.23 % |
| Transversion |
C>A |
Passed |
101378 |
4.57 % |
| Transversion |
T>G |
Passed |
94492 |
4.26 % |
| Transversion |
G>T |
Passed |
99533 |
4.49 % |
| Transversion |
A>T |
Passed |
78336 |
3.53 % |
| Transversion |
T>A |
Passed |
78409 |
3.53 % |
| Transversion |
C>G |
Passed |
103012 |
4.64 % |
| Transversion |
G>C |
Passed |
102302 |
4.61 % |
| |
|
|
|
|
| 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 |
1.68 |
10595009 |
6297643 |
| Passed |
1.95 |
1466781 |
751298 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |