/EXTERNAL McGill EMC/variants/K006133_1_lane_gembs
BACK
SAMPLE K006133_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1148746847 |
897148616 |
78.10 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1148746847 |
100% |
1134993088 |
98.80 % |
13753759 |
1.20 % |
| |
|
|
|
|
|
|
| Passed |
898761803 |
78.24 % |
894875505 |
78.84 % |
3886298 |
0.43 % |
| Filtered |
249985044 |
21.76 % |
240117583 |
21.16 % |
9867461 |
1.10 % |
| |
|
|
|
|
|
|
| q20 |
215975321 |
86.40 % |
214749657 |
89.44 % |
1225664 |
12.42 % |
| q20,qd2 |
14211837 |
5.69 % |
5950324 |
2.48 % |
8261513 |
83.72 % |
| q20,mq40 |
13880561 |
5.55 % |
13790469 |
5.74 % |
90092 |
0.91 % |
| q20,qd2,mq40 |
3353061 |
1.34 % |
3250608 |
1.35 % |
102453 |
1.04 % |
| mq40 |
1743735 |
0.70 % |
1589444 |
0.66 % |
154291 |
1.56 % |
| qd2 |
797789 |
0.32 % |
769481 |
0.32 % |
28308 |
0.29 % |
| qd2,mq40 |
22341 |
0.01 % |
17600 |
0.01 % |
4741 |
0.05 % |
| qd2,fs60,mq40 |
190 |
0.00 % |
0 |
0.00 % |
190 |
0.00 % |
| fs60,mq40 |
97 |
0.00 % |
0 |
0.00 % |
97 |
0.00 % |
| qd2,fs60 |
82 |
0.00 % |
0 |
0.00 % |
82 |
0.00 % |
| fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| q20,qd2,fs60,mq40 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| q20,qd2,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
5063731 |
32.98 % |
| Transition |
G>A |
All |
1199470 |
7.81 % |
| Transition |
T>C |
All |
5042528 |
32.84 % |
| Transition |
C>T |
All |
1207073 |
7.86 % |
| Transversion |
A>C |
All |
214070 |
1.39 % |
| Transversion |
C>A |
All |
605882 |
3.95 % |
| Transversion |
T>G |
All |
217112 |
1.41 % |
| Transversion |
G>T |
All |
591170 |
3.85 % |
| Transversion |
A>T |
All |
400505 |
2.61 % |
| Transversion |
T>A |
All |
392196 |
2.55 % |
| Transversion |
C>G |
All |
210325 |
1.37 % |
| Transversion |
G>C |
All |
210248 |
1.37 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
546390 |
16.78 % |
| Transition |
G>A |
Passed |
525550 |
16.14 % |
| Transition |
T>C |
Passed |
543502 |
16.69 % |
| Transition |
C>T |
Passed |
527216 |
16.19 % |
| Transversion |
A>C |
Passed |
138155 |
4.24 % |
| Transversion |
C>A |
Passed |
149656 |
4.60 % |
| Transversion |
T>G |
Passed |
139346 |
4.28 % |
| Transversion |
G>T |
Passed |
148615 |
4.56 % |
| Transversion |
A>T |
Passed |
127964 |
3.93 % |
| Transversion |
T>A |
Passed |
128000 |
3.93 % |
| Transversion |
C>G |
Passed |
140457 |
4.31 % |
| Transversion |
G>C |
Passed |
141378 |
4.34 % |
| |
|
|
|
|
| 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 |
4.40 |
12512802 |
2841508 |
| Passed |
1.92 |
2142658 |
1113571 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |