/EXTERNAL CREST/variants/K006476_1_lane_gembs
BACK
SAMPLE K006476_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1179091899 |
215259953 |
18.26 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1179091899 |
100% |
1093358044 |
92.73 % |
85733855 |
7.27 % |
| |
|
|
|
|
|
|
| Passed |
236951630 |
20.10 % |
212907627 |
19.47 % |
24044003 |
10.15 % |
| Filtered |
942140269 |
79.90 % |
880450417 |
80.53 % |
61689852 |
26.03 % |
| |
|
|
|
|
|
|
| q20 |
793604818 |
84.23 % |
772128514 |
87.70 % |
21476304 |
34.81 % |
| q20,qd2 |
68126708 |
7.23 % |
32246547 |
3.66 % |
35880161 |
58.16 % |
| q20,mq40 |
62979556 |
6.68 % |
61622280 |
7.00 % |
1357276 |
2.20 % |
| q20,qd2,mq40 |
10518676 |
1.12 % |
9265492 |
1.05 % |
1253184 |
2.03 % |
| mq40 |
6655110 |
0.71 % |
4952796 |
0.56 % |
1702314 |
2.76 % |
| qd2 |
245132 |
0.03 % |
227165 |
0.03 % |
17967 |
0.03 % |
| qd2,mq40 |
10200 |
0.00 % |
7623 |
0.00 % |
2577 |
0.00 % |
| fs60,mq40 |
50 |
0.00 % |
0 |
0.00 % |
50 |
0.00 % |
| fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| 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 |
14343341 |
16.13 % |
| Transition |
G>A |
All |
6761638 |
7.60 % |
| Transition |
T>C |
All |
13378657 |
15.05 % |
| Transition |
C>T |
All |
4136292 |
4.65 % |
| Transversion |
A>C |
All |
2631450 |
2.96 % |
| Transversion |
C>A |
All |
7372689 |
8.29 % |
| Transversion |
T>G |
All |
5033166 |
5.66 % |
| Transversion |
G>T |
All |
7873492 |
8.85 % |
| Transversion |
A>T |
All |
11385813 |
12.80 % |
| Transversion |
T>A |
All |
10565397 |
11.88 % |
| Transversion |
C>G |
All |
3440717 |
3.87 % |
| Transversion |
G>C |
All |
1996936 |
2.25 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
449454 |
18.11 % |
| Transition |
G>A |
Passed |
282669 |
11.39 % |
| Transition |
T>C |
Passed |
419022 |
16.88 % |
| Transition |
C>T |
Passed |
158488 |
6.38 % |
| Transversion |
A>C |
Passed |
109388 |
4.41 % |
| Transversion |
C>A |
Passed |
166529 |
6.71 % |
| Transversion |
T>G |
Passed |
214468 |
8.64 % |
| Transversion |
G>T |
Passed |
99569 |
4.01 % |
| Transversion |
A>T |
Passed |
102604 |
4.13 % |
| Transversion |
T>A |
Passed |
205585 |
8.28 % |
| Transversion |
C>G |
Passed |
169256 |
6.82 % |
| Transversion |
G>C |
Passed |
105389 |
4.25 % |
| |
|
|
|
|
| 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 |
0.77 |
38619928 |
50299660 |
| Passed |
1.12 |
1309633 |
1172788 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |