/EXTERNAL McGill EMC/variants/K006216_1_lane_gembs
BACK
SAMPLE K006216_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1160678411 |
583993701 |
50.31 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1160678411 |
100% |
1134115855 |
97.71 % |
26562556 |
2.29 % |
| |
|
|
|
|
|
|
| Passed |
589380361 |
50.78 % |
581146150 |
51.24 % |
8234211 |
1.40 % |
| Filtered |
571298050 |
49.22 % |
552969705 |
48.76 % |
18328345 |
3.11 % |
| |
|
|
|
|
|
|
| q20 |
525400268 |
91.97 % |
521438540 |
94.30 % |
3961728 |
21.62 % |
| q20,qd2 |
25225911 |
4.42 % |
11315733 |
2.05 % |
13910178 |
75.89 % |
| q20,mq40 |
15392651 |
2.69 % |
15287229 |
2.76 % |
105422 |
0.58 % |
| q20,qd2,mq40 |
3551586 |
0.62 % |
3417839 |
0.62 % |
133747 |
0.73 % |
| mq40 |
1081361 |
0.19 % |
895273 |
0.16 % |
186088 |
1.02 % |
| qd2 |
627962 |
0.11 % |
600790 |
0.11 % |
27172 |
0.15 % |
| qd2,mq40 |
17899 |
0.00 % |
14301 |
0.00 % |
3598 |
0.02 % |
| qd2,fs60,mq40 |
182 |
0.00 % |
0 |
0.00 % |
182 |
0.00 % |
| qd2,fs60 |
98 |
0.00 % |
0 |
0.00 % |
98 |
0.00 % |
| fs60,mq40 |
76 |
0.00 % |
0 |
0.00 % |
76 |
0.00 % |
| fs60 |
29 |
0.00 % |
0 |
0.00 % |
29 |
0.00 % |
| q20,qd2,fs60,mq40 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,qd2,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
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 |
9223547 |
33.21 % |
| Transition |
G>A |
All |
1283431 |
4.62 % |
| Transition |
T>C |
All |
9179026 |
33.05 % |
| Transition |
C>T |
All |
1293379 |
4.66 % |
| Transversion |
A>C |
All |
272525 |
0.98 % |
| Transversion |
C>A |
All |
2201387 |
7.93 % |
| Transversion |
T>G |
All |
276257 |
0.99 % |
| Transversion |
G>T |
All |
2183072 |
7.86 % |
| Transversion |
A>T |
All |
639705 |
2.30 % |
| Transversion |
T>A |
All |
627437 |
2.26 % |
| Transversion |
C>G |
All |
297235 |
1.07 % |
| Transversion |
G>C |
All |
292743 |
1.05 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
547960 |
16.89 % |
| Transition |
G>A |
Passed |
478978 |
14.77 % |
| Transition |
T>C |
Passed |
549375 |
16.94 % |
| Transition |
C>T |
Passed |
483202 |
14.90 % |
| Transversion |
A>C |
Passed |
146492 |
4.52 % |
| Transversion |
C>A |
Passed |
157817 |
4.87 % |
| Transversion |
T>G |
Passed |
146458 |
4.52 % |
| Transversion |
G>T |
Passed |
158769 |
4.90 % |
| Transversion |
A>T |
Passed |
138197 |
4.26 % |
| Transversion |
T>A |
Passed |
138273 |
4.26 % |
| Transversion |
C>G |
Passed |
148769 |
4.59 % |
| Transversion |
G>C |
Passed |
149153 |
4.60 % |
| |
|
|
|
|
| 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 |
3.09 |
20979383 |
6790361 |
| Passed |
1.74 |
2059515 |
1183928 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |