/EXTERNAL McGill EMC/variants/K006185_1_lane_gembs
BACK
SAMPLE K006185_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170364167 |
206927774 |
17.68 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170364167 |
100% |
1100720234 |
94.05 % |
69643933 |
5.95 % |
| |
|
|
|
|
|
|
| Passed |
223829207 |
19.12 % |
203917232 |
18.53 % |
19911975 |
8.90 % |
| Filtered |
946534960 |
80.88 % |
896803002 |
81.47 % |
49731958 |
22.22 % |
| |
|
|
|
|
|
|
| q20 |
847713381 |
89.56 % |
837388918 |
93.37 % |
10324463 |
20.76 % |
| q20,qd2 |
53210698 |
5.62 % |
18457118 |
2.06 % |
34753580 |
69.88 % |
| q20,mq40 |
33439232 |
3.53 % |
32546804 |
3.63 % |
892428 |
1.79 % |
| q20,qd2,mq40 |
6847222 |
0.72 % |
5514522 |
0.61 % |
1332700 |
2.68 % |
| mq40 |
4999390 |
0.53 % |
2605012 |
0.29 % |
2394378 |
4.81 % |
| qd2 |
285585 |
0.03 % |
259455 |
0.03 % |
26130 |
0.05 % |
| qd2,mq40 |
38977 |
0.00 % |
31173 |
0.00 % |
7804 |
0.02 % |
| qd2,fs60,mq40 |
296 |
0.00 % |
0 |
0.00 % |
296 |
0.00 % |
| fs60,mq40 |
79 |
0.00 % |
0 |
0.00 % |
79 |
0.00 % |
| qd2,fs60 |
75 |
0.00 % |
0 |
0.00 % |
75 |
0.00 % |
| q20,qd2,fs60,mq40 |
17 |
0.00 % |
0 |
0.00 % |
17 |
0.00 % |
| fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
11746845 |
16.29 % |
| Transition |
G>A |
All |
4553116 |
6.31 % |
| Transition |
T>C |
All |
11246501 |
15.60 % |
| Transition |
C>T |
All |
4110433 |
5.70 % |
| Transversion |
A>C |
All |
1197707 |
1.66 % |
| Transversion |
C>A |
All |
13927135 |
19.31 % |
| Transversion |
T>G |
All |
1339286 |
1.86 % |
| Transversion |
G>T |
All |
13857156 |
19.22 % |
| Transversion |
A>T |
All |
3758349 |
5.21 % |
| Transversion |
T>A |
All |
3641880 |
5.05 % |
| Transversion |
C>G |
All |
1425941 |
1.98 % |
| Transversion |
G>C |
All |
1307933 |
1.81 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
589273 |
18.53 % |
| Transition |
G>A |
Passed |
358156 |
11.26 % |
| Transition |
T>C |
Passed |
571600 |
17.98 % |
| Transition |
C>T |
Passed |
348246 |
10.95 % |
| Transversion |
A>C |
Passed |
161111 |
5.07 % |
| Transversion |
C>A |
Passed |
166300 |
5.23 % |
| Transversion |
T>G |
Passed |
164134 |
5.16 % |
| Transversion |
G>T |
Passed |
159281 |
5.01 % |
| Transversion |
A>T |
Passed |
143669 |
4.52 % |
| Transversion |
T>A |
Passed |
144962 |
4.56 % |
| Transversion |
C>G |
Passed |
188222 |
5.92 % |
| Transversion |
G>C |
Passed |
184467 |
5.80 % |
| |
|
|
|
|
| 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 |
0.78 |
31656895 |
40455387 |
| Passed |
1.42 |
1867275 |
1312146 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |