/EXTERNAL McGill EMC/variants/K006209_1_lane_gembs
BACK
SAMPLE K006209_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1175132649 |
1077470410 |
91.69 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1175132649 |
100% |
1155405606 |
98.32 % |
19727043 |
1.68 % |
| |
|
|
|
|
|
|
| Passed |
1078312784 |
91.76 % |
1073842432 |
92.94 % |
4470352 |
0.41 % |
| Filtered |
96819865 |
8.24 % |
81563174 |
7.06 % |
15256691 |
1.41 % |
| |
|
|
|
|
|
|
| q20 |
48394981 |
49.98 % |
46822969 |
57.41 % |
1572012 |
10.30 % |
| q20,qd2 |
17026141 |
17.59 % |
5795839 |
7.11 % |
11230302 |
73.61 % |
| q20,mq40 |
13825264 |
14.28 % |
13466485 |
16.51 % |
358779 |
2.35 % |
| qd2 |
7561276 |
7.81 % |
6276828 |
7.70 % |
1284448 |
8.42 % |
| mq40 |
6781812 |
7.00 % |
6435444 |
7.89 % |
346368 |
2.27 % |
| q20,qd2,mq40 |
3136089 |
3.24 % |
2686767 |
3.29 % |
449322 |
2.95 % |
| qd2,mq40 |
92964 |
0.10 % |
78842 |
0.10 % |
14122 |
0.09 % |
| qd2,fs60,mq40 |
566 |
0.00 % |
0 |
0.00 % |
566 |
0.00 % |
| qd2,fs60 |
285 |
0.00 % |
0 |
0.00 % |
285 |
0.00 % |
| fs60,mq40 |
238 |
0.00 % |
0 |
0.00 % |
238 |
0.00 % |
| fs60 |
165 |
0.00 % |
0 |
0.00 % |
165 |
0.00 % |
| q20,qd2,fs60,mq40 |
55 |
0.00 % |
0 |
0.00 % |
55 |
0.00 % |
| q20,qd2,fs60 |
26 |
0.00 % |
0 |
0.00 % |
26 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
7379521 |
34.34 % |
| Transition |
G>A |
All |
1099950 |
5.12 % |
| Transition |
T>C |
All |
7205254 |
33.53 % |
| Transition |
C>T |
All |
1110549 |
5.17 % |
| Transversion |
A>C |
All |
398697 |
1.86 % |
| Transversion |
C>A |
All |
926701 |
4.31 % |
| Transversion |
T>G |
All |
403291 |
1.88 % |
| Transversion |
G>T |
All |
935128 |
4.35 % |
| Transversion |
A>T |
All |
690477 |
3.21 % |
| Transversion |
T>A |
All |
685570 |
3.19 % |
| Transversion |
C>G |
All |
326870 |
1.52 % |
| Transversion |
G>C |
All |
325269 |
1.51 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1170884 |
24.02 % |
| Transition |
G>A |
Passed |
617156 |
12.66 % |
| Transition |
T>C |
Passed |
1137623 |
23.34 % |
| Transition |
C>T |
Passed |
619941 |
12.72 % |
| Transversion |
A>C |
Passed |
174360 |
3.58 % |
| Transversion |
C>A |
Passed |
169934 |
3.49 % |
| Transversion |
T>G |
Passed |
175575 |
3.60 % |
| Transversion |
G>T |
Passed |
168801 |
3.46 % |
| Transversion |
A>T |
Passed |
151287 |
3.10 % |
| Transversion |
T>A |
Passed |
151174 |
3.10 % |
| Transversion |
C>G |
Passed |
168692 |
3.46 % |
| Transversion |
G>C |
Passed |
168825 |
3.46 % |
| |
|
|
|
|
| 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 |
3.58 |
16795274 |
4692003 |
| Passed |
2.67 |
3545604 |
1328648 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |