/EXTERNAL McGill EMC/variants/K006214_1_lane_gembs
BACK
SAMPLE K006214_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1154502001 |
993495658 |
86.05 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1154502001 |
100% |
1137279167 |
98.51 % |
17222834 |
1.49 % |
| |
|
|
|
|
|
|
| Passed |
994760764 |
86.16 % |
989114915 |
86.97 % |
5645849 |
0.57 % |
| Filtered |
159741237 |
13.84 % |
148164252 |
13.03 % |
11576985 |
1.16 % |
| |
|
|
|
|
|
|
| q20 |
124069149 |
77.67 % |
122740944 |
82.84 % |
1328205 |
11.47 % |
| q20,qd2 |
15008031 |
9.40 % |
5572382 |
3.76 % |
9435649 |
81.50 % |
| q20,mq40 |
12310616 |
7.71 % |
12205601 |
8.24 % |
105015 |
0.91 % |
| q20,qd2,mq40 |
2939969 |
1.84 % |
2775386 |
1.87 % |
164583 |
1.42 % |
| mq40 |
2785627 |
1.74 % |
2571405 |
1.74 % |
214222 |
1.85 % |
| qd2 |
2598773 |
1.63 % |
2275937 |
1.54 % |
322836 |
2.79 % |
| qd2,mq40 |
28333 |
0.02 % |
22597 |
0.02 % |
5736 |
0.05 % |
| qd2,fs60,mq40 |
348 |
0.00 % |
0 |
0.00 % |
348 |
0.00 % |
| qd2,fs60 |
147 |
0.00 % |
0 |
0.00 % |
147 |
0.00 % |
| fs60,mq40 |
138 |
0.00 % |
0 |
0.00 % |
138 |
0.00 % |
| fs60 |
62 |
0.00 % |
0 |
0.00 % |
62 |
0.00 % |
| q20,qd2,fs60,mq40 |
31 |
0.00 % |
0 |
0.00 % |
31 |
0.00 % |
| q20,qd2,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
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 |
6022446 |
33.37 % |
| Transition |
G>A |
All |
1346639 |
7.46 % |
| Transition |
T>C |
All |
5938338 |
32.90 % |
| Transition |
C>T |
All |
1346886 |
7.46 % |
| Transversion |
A>C |
All |
274490 |
1.52 % |
| Transversion |
C>A |
All |
706935 |
3.92 % |
| Transversion |
T>G |
All |
276168 |
1.53 % |
| Transversion |
G>T |
All |
699999 |
3.88 % |
| Transversion |
A>T |
All |
442108 |
2.45 % |
| Transversion |
T>A |
All |
426777 |
2.36 % |
| Transversion |
C>G |
All |
284932 |
1.58 % |
| Transversion |
G>C |
All |
283653 |
1.57 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
826491 |
17.10 % |
| Transition |
G>A |
Passed |
766438 |
15.86 % |
| Transition |
T>C |
Passed |
828052 |
17.13 % |
| Transition |
C>T |
Passed |
772877 |
15.99 % |
| Transversion |
A>C |
Passed |
202584 |
4.19 % |
| Transversion |
C>A |
Passed |
218781 |
4.53 % |
| Transversion |
T>G |
Passed |
202760 |
4.20 % |
| Transversion |
G>T |
Passed |
219495 |
4.54 % |
| Transversion |
A>T |
Passed |
189264 |
3.92 % |
| Transversion |
T>A |
Passed |
187810 |
3.89 % |
| Transversion |
C>G |
Passed |
208973 |
4.32 % |
| Transversion |
G>C |
Passed |
209458 |
4.33 % |
| |
|
|
|
|
| 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 |
4.32 |
14654309 |
3395062 |
| Passed |
1.95 |
3193858 |
1639125 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |