/EXTERNAL McGill EMC/variants/K006215_1_lane_gembs
BACK
SAMPLE K006215_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1161478620 |
821131864 |
70.70 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1161478620 |
100% |
1138756263 |
98.04 % |
22722357 |
1.96 % |
| |
|
|
|
|
|
|
| Passed |
823913217 |
70.94 % |
817361469 |
71.78 % |
6551748 |
0.80 % |
| Filtered |
337565403 |
29.06 % |
321394794 |
28.22 % |
16170609 |
1.96 % |
| |
|
|
|
|
|
|
| q20 |
292498238 |
86.65 % |
289967365 |
90.22 % |
2530873 |
15.65 % |
| q20,qd2 |
22544198 |
6.68 % |
9541924 |
2.97 % |
13002274 |
80.41 % |
| q20,mq40 |
14869558 |
4.40 % |
14759138 |
4.59 % |
110420 |
0.68 % |
| q20,qd2,mq40 |
3214953 |
0.95 % |
3038868 |
0.95 % |
176085 |
1.09 % |
| qd2 |
2287300 |
0.68 % |
2149283 |
0.67 % |
138017 |
0.85 % |
| mq40 |
2126261 |
0.63 % |
1918678 |
0.60 % |
207583 |
1.28 % |
| qd2,mq40 |
24233 |
0.01 % |
19538 |
0.01 % |
4695 |
0.03 % |
| qd2,fs60,mq40 |
307 |
0.00 % |
0 |
0.00 % |
307 |
0.00 % |
| qd2,fs60 |
142 |
0.00 % |
0 |
0.00 % |
142 |
0.00 % |
| fs60,mq40 |
126 |
0.00 % |
0 |
0.00 % |
126 |
0.00 % |
| fs60 |
48 |
0.00 % |
0 |
0.00 % |
48 |
0.00 % |
| q20,qd2,fs60,mq40 |
27 |
0.00 % |
0 |
0.00 % |
27 |
0.00 % |
| q20,qd2,fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
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 |
7932939 |
33.52 % |
| Transition |
G>A |
All |
1377665 |
5.82 % |
| Transition |
T>C |
All |
7840109 |
33.12 % |
| Transition |
C>T |
All |
1375726 |
5.81 % |
| Transversion |
A>C |
All |
264751 |
1.12 % |
| Transversion |
C>A |
All |
1517764 |
6.41 % |
| Transversion |
T>G |
All |
270077 |
1.14 % |
| Transversion |
G>T |
All |
1511646 |
6.39 % |
| Transversion |
A>T |
All |
509819 |
2.15 % |
| Transversion |
T>A |
All |
495506 |
2.09 % |
| Transversion |
C>G |
All |
288305 |
1.22 % |
| Transversion |
G>C |
All |
284240 |
1.20 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
718088 |
17.05 % |
| Transition |
G>A |
Passed |
649331 |
15.42 % |
| Transition |
T>C |
Passed |
720765 |
17.11 % |
| Transition |
C>T |
Passed |
655505 |
15.56 % |
| Transversion |
A>C |
Passed |
181015 |
4.30 % |
| Transversion |
C>A |
Passed |
196061 |
4.66 % |
| Transversion |
T>G |
Passed |
181344 |
4.31 % |
| Transversion |
G>T |
Passed |
196305 |
4.66 % |
| Transversion |
A>T |
Passed |
170958 |
4.06 % |
| Transversion |
T>A |
Passed |
170307 |
4.04 % |
| Transversion |
C>G |
Passed |
185784 |
4.41 % |
| Transversion |
G>C |
Passed |
186197 |
4.42 % |
| |
|
|
|
|
| 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 |
3.60 |
18526439 |
5142108 |
| Passed |
1.87 |
2743689 |
1467971 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |