/EXTERNAL McGill EMC/variants/K006139_1_lane_gembs
BACK
SAMPLE K006139_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1129343277 |
66081290 |
5.85 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1129343277 |
100% |
1108236003 |
98.13 % |
21107274 |
1.87 % |
| |
|
|
|
|
|
|
| Passed |
73009151 |
6.46 % |
64642819 |
5.83 % |
8366332 |
11.46 % |
| Filtered |
1056334126 |
93.54 % |
1043593184 |
94.17 % |
12740942 |
17.45 % |
| |
|
|
|
|
|
|
| q20 |
973488123 |
92.16 % |
968573772 |
92.81 % |
4914351 |
38.57 % |
| q20,qd2 |
52755502 |
4.99 % |
45741827 |
4.38 % |
7013675 |
55.05 % |
| q20,mq40 |
21701501 |
2.05 % |
21472872 |
2.06 % |
228629 |
1.79 % |
| q20,qd2,mq40 |
7659021 |
0.73 % |
7480416 |
0.72 % |
178605 |
1.40 % |
| mq40 |
697623 |
0.07 % |
296769 |
0.03 % |
400854 |
3.15 % |
| qd2 |
17975 |
0.00 % |
15956 |
0.00 % |
2019 |
0.02 % |
| qd2,mq40 |
14211 |
0.00 % |
11572 |
0.00 % |
2639 |
0.02 % |
| qd2,fs60,mq40 |
100 |
0.00 % |
0 |
0.00 % |
100 |
0.00 % |
| fs60,mq40 |
49 |
0.00 % |
0 |
0.00 % |
49 |
0.00 % |
| qd2,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| q20,qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 % |
| q20,qd2,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 |
4593853 |
19.32 % |
| Transition |
G>A |
All |
1409211 |
5.93 % |
| Transition |
T>C |
All |
4555120 |
19.16 % |
| Transition |
C>T |
All |
1332322 |
5.60 % |
| Transversion |
A>C |
All |
934017 |
3.93 % |
| Transversion |
C>A |
All |
2920372 |
12.28 % |
| Transversion |
T>G |
All |
1043543 |
4.39 % |
| Transversion |
G>T |
All |
2958893 |
12.45 % |
| Transversion |
A>T |
All |
1233840 |
5.19 % |
| Transversion |
T>A |
All |
1244147 |
5.23 % |
| Transversion |
C>G |
All |
808994 |
3.40 % |
| Transversion |
G>C |
All |
740572 |
3.11 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
452414 |
30.27 % |
| Transition |
G>A |
Passed |
140171 |
9.38 % |
| Transition |
T>C |
Passed |
341591 |
22.85 % |
| Transition |
C>T |
Passed |
119409 |
7.99 % |
| Transversion |
A>C |
Passed |
49769 |
3.33 % |
| Transversion |
C>A |
Passed |
63111 |
4.22 % |
| Transversion |
T>G |
Passed |
54294 |
3.63 % |
| Transversion |
G>T |
Passed |
55247 |
3.70 % |
| Transversion |
A>T |
Passed |
47338 |
3.17 % |
| Transversion |
T>A |
Passed |
53588 |
3.59 % |
| Transversion |
C>G |
Passed |
61364 |
4.11 % |
| Transversion |
G>C |
Passed |
56359 |
3.77 % |
| |
|
|
|
|
| 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 |
1.00 |
11890506 |
11884378 |
| Passed |
2.39 |
1053585 |
441070 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |