/EXTERNAL McGill EMC/variants/K006148_1_lane_gembs
BACK
SAMPLE K006148_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1136149172 |
163646931 |
14.40 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1136149172 |
100% |
1123018268 |
98.84 % |
13130904 |
1.16 % |
| |
|
|
|
|
|
|
| Passed |
168491712 |
14.83 % |
162502709 |
14.47 % |
5989003 |
3.55 % |
| Filtered |
967657460 |
85.17 % |
960515559 |
85.53 % |
7141901 |
4.24 % |
| |
|
|
|
|
|
|
| q20 |
924905553 |
95.58 % |
922413020 |
96.03 % |
2492533 |
34.90 % |
| q20,qd2 |
20962071 |
2.17 % |
16574037 |
1.73 % |
4388034 |
61.44 % |
| q20,mq40 |
16380346 |
1.69 % |
16302834 |
1.70 % |
77512 |
1.09 % |
| q20,qd2,mq40 |
5061389 |
0.52 % |
4992484 |
0.52 % |
68905 |
0.96 % |
| mq40 |
308669 |
0.03 % |
199579 |
0.02 % |
109090 |
1.53 % |
| qd2 |
26183 |
0.00 % |
23220 |
0.00 % |
2963 |
0.04 % |
| qd2,mq40 |
13019 |
0.00 % |
10385 |
0.00 % |
2634 |
0.04 % |
| qd2,fs60,mq40 |
125 |
0.00 % |
0 |
0.00 % |
125 |
0.00 % |
| qd2,fs60 |
43 |
0.00 % |
0 |
0.00 % |
43 |
0.00 % |
| fs60,mq40 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| q20,qd2,fs60,mq40 |
9 |
0.00 % |
0 |
0.00 % |
9 |
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 |
4157221 |
27.76 % |
| Transition |
G>A |
All |
875887 |
5.85 % |
| Transition |
T>C |
All |
3993553 |
26.66 % |
| Transition |
C>T |
All |
881071 |
5.88 % |
| Transversion |
A>C |
All |
237367 |
1.58 % |
| Transversion |
C>A |
All |
1203530 |
8.04 % |
| Transversion |
T>G |
All |
268378 |
1.79 % |
| Transversion |
G>T |
All |
1169616 |
7.81 % |
| Transversion |
A>T |
All |
850326 |
5.68 % |
| Transversion |
T>A |
All |
877895 |
5.86 % |
| Transversion |
C>G |
All |
240301 |
1.60 % |
| Transversion |
G>C |
All |
222171 |
1.48 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
193683 |
14.94 % |
| Transition |
G>A |
Passed |
180734 |
13.94 % |
| Transition |
T>C |
Passed |
199383 |
15.38 % |
| Transition |
C>T |
Passed |
184355 |
14.22 % |
| Transversion |
A>C |
Passed |
66853 |
5.16 % |
| Transversion |
C>A |
Passed |
71022 |
5.48 % |
| Transversion |
T>G |
Passed |
67498 |
5.21 % |
| Transversion |
G>T |
Passed |
71593 |
5.52 % |
| Transversion |
A>T |
Passed |
63634 |
4.91 % |
| Transversion |
T>A |
Passed |
63642 |
4.91 % |
| Transversion |
C>G |
Passed |
66922 |
5.16 % |
| Transversion |
G>C |
Passed |
67237 |
5.19 % |
| |
|
|
|
|
| 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 |
1.95 |
9907732 |
5069584 |
| Passed |
1.41 |
758155 |
538401 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |