/EXTERNAL McGill EMC/variants/K006158_1_lane_gembs
BACK
SAMPLE K006158_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1150629931 |
783921205 |
68.13 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1150629931 |
100% |
1135271612 |
98.67 % |
15358319 |
1.33 % |
| |
|
|
|
|
|
|
| Passed |
785611290 |
68.28 % |
781699563 |
68.86 % |
3911727 |
0.50 % |
| Filtered |
365018641 |
31.72 % |
353572049 |
31.14 % |
11446592 |
1.46 % |
| |
|
|
|
|
|
|
| q20 |
326384059 |
89.42 % |
324112282 |
91.67 % |
2271777 |
19.85 % |
| q20,qd2 |
16498205 |
4.52 % |
7803035 |
2.21 % |
8695170 |
75.96 % |
| q20,mq40 |
15746149 |
4.31 % |
15604857 |
4.41 % |
141292 |
1.23 % |
| q20,qd2,mq40 |
3908357 |
1.07 % |
3772635 |
1.07 % |
135722 |
1.19 % |
| mq40 |
1468492 |
0.40 % |
1308257 |
0.37 % |
160235 |
1.40 % |
| qd2 |
990409 |
0.27 % |
952995 |
0.27 % |
37414 |
0.33 % |
| qd2,mq40 |
22534 |
0.01 % |
17988 |
0.01 % |
4546 |
0.04 % |
| qd2,fs60,mq40 |
202 |
0.00 % |
0 |
0.00 % |
202 |
0.00 % |
| fs60,mq40 |
92 |
0.00 % |
0 |
0.00 % |
92 |
0.00 % |
| qd2,fs60 |
87 |
0.00 % |
0 |
0.00 % |
87 |
0.00 % |
| fs60 |
26 |
0.00 % |
0 |
0.00 % |
26 |
0.00 % |
| q20,qd2,fs60,mq40 |
26 |
0.00 % |
0 |
0.00 % |
26 |
0.00 % |
| q20,qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
5233482 |
30.76 % |
| Transition |
G>A |
All |
1331425 |
7.83 % |
| Transition |
T>C |
All |
5018163 |
29.50 % |
| Transition |
C>T |
All |
1349905 |
7.93 % |
| Transversion |
A>C |
All |
313630 |
1.84 % |
| Transversion |
C>A |
All |
959307 |
5.64 % |
| Transversion |
T>G |
All |
313776 |
1.84 % |
| Transversion |
G>T |
All |
902422 |
5.30 % |
| Transversion |
A>T |
All |
495965 |
2.92 % |
| Transversion |
T>A |
All |
519376 |
3.05 % |
| Transversion |
C>G |
All |
289289 |
1.70 % |
| Transversion |
G>C |
All |
286143 |
1.68 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
533596 |
17.38 % |
| Transition |
G>A |
Passed |
478711 |
15.59 % |
| Transition |
T>C |
Passed |
544239 |
17.73 % |
| Transition |
C>T |
Passed |
487254 |
15.87 % |
| Transversion |
A>C |
Passed |
128716 |
4.19 % |
| Transversion |
C>A |
Passed |
136491 |
4.45 % |
| Transversion |
T>G |
Passed |
128798 |
4.20 % |
| Transversion |
G>T |
Passed |
135790 |
4.42 % |
| Transversion |
A>T |
Passed |
116961 |
3.81 % |
| Transversion |
T>A |
Passed |
117077 |
3.81 % |
| Transversion |
C>G |
Passed |
130632 |
4.26 % |
| Transversion |
G>C |
Passed |
131624 |
4.29 % |
| |
|
|
|
|
| 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 |
3.17 |
12932975 |
4079908 |
| Passed |
1.99 |
2043800 |
1026089 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |