/EXTERNAL McGill EMC/variants/K006218_1_lane_gembs
BACK
SAMPLE K006218_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1152365853 |
919024407 |
79.75 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1152365853 |
100% |
1137423541 |
98.70 % |
14942312 |
1.30 % |
| |
|
|
|
|
|
|
| Passed |
920639755 |
79.89 % |
916621494 |
80.59 % |
4018261 |
0.44 % |
| Filtered |
231726098 |
20.11 % |
220802047 |
19.41 % |
10924051 |
1.19 % |
| |
|
|
|
|
|
|
| q20 |
196591986 |
84.84 % |
194874921 |
88.26 % |
1717065 |
15.72 % |
| q20,qd2 |
15196582 |
6.56 % |
6501041 |
2.94 % |
8695541 |
79.60 % |
| q20,mq40 |
12033270 |
5.19 % |
11928645 |
5.40 % |
104625 |
0.96 % |
| q20,qd2,mq40 |
3217192 |
1.39 % |
3082537 |
1.40 % |
134655 |
1.23 % |
| qd2 |
2579196 |
1.11 % |
2485146 |
1.13 % |
94050 |
0.86 % |
| mq40 |
2072039 |
0.89 % |
1902020 |
0.86 % |
170019 |
1.56 % |
| qd2,mq40 |
34856 |
0.02 % |
27737 |
0.01 % |
7119 |
0.07 % |
| qd2,fs60,mq40 |
509 |
0.00 % |
0 |
0.00 % |
509 |
0.00 % |
| fs60,mq40 |
180 |
0.00 % |
0 |
0.00 % |
180 |
0.00 % |
| qd2,fs60 |
138 |
0.00 % |
0 |
0.00 % |
138 |
0.00 % |
| fs60 |
101 |
0.00 % |
0 |
0.00 % |
101 |
0.00 % |
| q20,qd2,fs60,mq40 |
33 |
0.00 % |
0 |
0.00 % |
33 |
0.00 % |
| q20,qd2,fs60 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
5668374 |
34.15 % |
| Transition |
G>A |
All |
1227117 |
7.39 % |
| Transition |
T>C |
All |
5356433 |
32.27 % |
| Transition |
C>T |
All |
1256233 |
7.57 % |
| Transversion |
A>C |
All |
216307 |
1.30 % |
| Transversion |
C>A |
All |
741206 |
4.47 % |
| Transversion |
T>G |
All |
226845 |
1.37 % |
| Transversion |
G>T |
All |
726749 |
4.38 % |
| Transversion |
A>T |
All |
365601 |
2.20 % |
| Transversion |
T>A |
All |
362339 |
2.18 % |
| Transversion |
C>G |
All |
230197 |
1.39 % |
| Transversion |
G>C |
All |
220210 |
1.33 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
594147 |
17.24 % |
| Transition |
G>A |
Passed |
561450 |
16.29 % |
| Transition |
T>C |
Passed |
586295 |
17.01 % |
| Transition |
C>T |
Passed |
568738 |
16.50 % |
| Transversion |
A>C |
Passed |
140418 |
4.07 % |
| Transversion |
C>A |
Passed |
154093 |
4.47 % |
| Transversion |
T>G |
Passed |
140601 |
4.08 % |
| Transversion |
G>T |
Passed |
153619 |
4.46 % |
| Transversion |
A>T |
Passed |
131508 |
3.82 % |
| Transversion |
T>A |
Passed |
130654 |
3.79 % |
| Transversion |
C>G |
Passed |
142323 |
4.13 % |
| Transversion |
G>C |
Passed |
142125 |
4.12 % |
| |
|
|
|
|
| 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 |
4.37 |
13508157 |
3089454 |
| Passed |
2.04 |
2310630 |
1135341 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |