/EXTERNAL McGill EMC/variants/K006161_1_lane_gembs
BACK
SAMPLE K006161_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1116914335 |
181161675 |
16.22 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1116914335 |
100% |
1105364510 |
98.97 % |
11549825 |
1.03 % |
| |
|
|
|
|
|
|
| Passed |
183514301 |
16.43 % |
180172838 |
16.30 % |
3341463 |
1.82 % |
| Filtered |
933400034 |
83.57 % |
925191672 |
83.70 % |
8208362 |
4.47 % |
| |
|
|
|
|
|
|
| q20 |
868143989 |
93.01 % |
865113206 |
93.51 % |
3030783 |
36.92 % |
| q20,qd2 |
42916292 |
4.60 % |
38012187 |
4.11 % |
4904105 |
59.75 % |
| q20,mq40 |
16844339 |
1.80 % |
16742624 |
1.81 % |
101715 |
1.24 % |
| q20,qd2,mq40 |
4907873 |
0.53 % |
4842436 |
0.52 % |
65437 |
0.80 % |
| mq40 |
351103 |
0.04 % |
255729 |
0.03 % |
95374 |
1.16 % |
| qd2 |
217990 |
0.02 % |
210775 |
0.02 % |
7215 |
0.09 % |
| qd2,mq40 |
18022 |
0.00 % |
14715 |
0.00 % |
3307 |
0.04 % |
| qd2,fs60,mq40 |
225 |
0.00 % |
0 |
0.00 % |
225 |
0.00 % |
| fs60,mq40 |
100 |
0.00 % |
0 |
0.00 % |
100 |
0.00 % |
| qd2,fs60 |
73 |
0.00 % |
0 |
0.00 % |
73 |
0.00 % |
| fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,qd2,fs60,mq40 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
2222426 |
16.50 % |
| Transition |
G>A |
All |
1218174 |
9.05 % |
| Transition |
T>C |
All |
2174159 |
16.15 % |
| Transition |
C>T |
All |
1218685 |
9.05 % |
| Transversion |
A>C |
All |
583147 |
4.33 % |
| Transversion |
C>A |
All |
1601012 |
11.89 % |
| Transversion |
T>G |
All |
584137 |
4.34 % |
| Transversion |
G>T |
All |
1585365 |
11.77 % |
| Transversion |
A>T |
All |
708229 |
5.26 % |
| Transversion |
T>A |
All |
708503 |
5.26 % |
| Transversion |
C>G |
All |
430904 |
3.20 % |
| Transversion |
G>C |
All |
431205 |
3.20 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
179700 |
15.09 % |
| Transition |
G>A |
Passed |
174277 |
14.64 % |
| Transition |
T>C |
Passed |
181820 |
15.27 % |
| Transition |
C>T |
Passed |
177140 |
14.88 % |
| Transversion |
A>C |
Passed |
59862 |
5.03 % |
| Transversion |
C>A |
Passed |
63368 |
5.32 % |
| Transversion |
T>G |
Passed |
60347 |
5.07 % |
| Transversion |
G>T |
Passed |
63104 |
5.30 % |
| Transversion |
A>T |
Passed |
58302 |
4.90 % |
| Transversion |
T>A |
Passed |
58152 |
4.88 % |
| Transversion |
C>G |
Passed |
57028 |
4.79 % |
| Transversion |
G>C |
Passed |
57367 |
4.82 % |
| |
|
|
|
|
| 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 |
1.03 |
6833444 |
6632502 |
| Passed |
1.49 |
712937 |
477530 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |