/EXTERNAL McGill EMC/variants/K006172_1_lane_gembs
BACK
SAMPLE K006172_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1159748552 |
74690342 |
6.44 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1159748552 |
100% |
1033813674 |
89.14 % |
125934878 |
10.86 % |
| |
|
|
|
|
|
|
| Passed |
81326911 |
7.01 % |
73210108 |
7.08 % |
8116803 |
9.98 % |
| Filtered |
1078421641 |
92.99 % |
960603566 |
92.92 % |
117818075 |
144.87 % |
| |
|
|
|
|
|
|
| q20 |
872817572 |
80.93 % |
847512719 |
88.23 % |
25304853 |
21.48 % |
| q20,qd2 |
134171567 |
12.44 % |
47359282 |
4.93 % |
86812285 |
73.68 % |
| q20,mq40 |
55705025 |
5.17 % |
53596766 |
5.58 % |
2108259 |
1.79 % |
| q20,qd2,mq40 |
14493246 |
1.34 % |
11341837 |
1.18 % |
3151409 |
2.67 % |
| mq40 |
1142560 |
0.11 % |
706423 |
0.07 % |
436137 |
0.37 % |
| qd2 |
68811 |
0.01 % |
67106 |
0.01 % |
1705 |
0.00 % |
| qd2,mq40 |
22546 |
0.00 % |
19433 |
0.00 % |
3113 |
0.00 % |
| fs60,mq40 |
126 |
0.00 % |
0 |
0.00 % |
126 |
0.00 % |
| qd2,fs60,mq40 |
108 |
0.00 % |
0 |
0.00 % |
108 |
0.00 % |
| q20,qd2,fs60,mq40 |
56 |
0.00 % |
0 |
0.00 % |
56 |
0.00 % |
| qd2,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
9309888 |
7.23 % |
| Transition |
G>A |
All |
2435146 |
1.89 % |
| Transition |
T>C |
All |
9155437 |
7.11 % |
| Transition |
C>T |
All |
2449891 |
1.90 % |
| Transversion |
A>C |
All |
4324152 |
3.36 % |
| Transversion |
C>A |
All |
42954965 |
33.34 % |
| Transversion |
T>G |
All |
4397610 |
3.41 % |
| Transversion |
G>T |
All |
42627735 |
33.09 % |
| Transversion |
A>T |
All |
3650162 |
2.83 % |
| Transversion |
T>A |
All |
3670026 |
2.85 % |
| Transversion |
C>G |
All |
1948255 |
1.51 % |
| Transversion |
G>C |
All |
1905856 |
1.48 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
170782 |
11.06 % |
| Transition |
G>A |
Passed |
133617 |
8.65 % |
| Transition |
T>C |
Passed |
172375 |
11.16 % |
| Transition |
C>T |
Passed |
136618 |
8.84 % |
| Transversion |
A>C |
Passed |
87673 |
5.68 % |
| Transversion |
C>A |
Passed |
152236 |
9.86 % |
| Transversion |
T>G |
Passed |
89387 |
5.79 % |
| Transversion |
G>T |
Passed |
149522 |
9.68 % |
| Transversion |
A>T |
Passed |
54864 |
3.55 % |
| Transversion |
T>A |
Passed |
54758 |
3.54 % |
| Transversion |
C>G |
Passed |
173597 |
11.24 % |
| Transversion |
G>C |
Passed |
169264 |
10.96 % |
| |
|
|
|
|
| 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 |
0.22 |
23350362 |
105478761 |
| Passed |
0.66 |
613392 |
931301 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |