/EXTERNAL CREST/variants/K006434_1_lane_gembs
BACK
SAMPLE K006434_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1209208784 |
738128032 |
61.04 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1209208784 |
100% |
1119612565 |
92.59 % |
89596219 |
7.41 % |
| |
|
|
|
|
|
|
| Passed |
750455807 |
62.06 % |
731157181 |
65.30 % |
19298626 |
2.57 % |
| Filtered |
458752977 |
37.94 % |
388455384 |
34.70 % |
70297593 |
9.37 % |
| |
|
|
|
|
|
|
| q20 |
301180846 |
65.65 % |
283459837 |
72.97 % |
17721009 |
25.21 % |
| q20,qd2 |
68403668 |
14.91 % |
22784209 |
5.87 % |
45619459 |
64.89 % |
| q20,mq40 |
42056784 |
9.17 % |
40362500 |
10.39 % |
1694284 |
2.41 % |
| mq40 |
29262549 |
6.38 % |
27313414 |
7.03 % |
1949135 |
2.77 % |
| qd2 |
10280501 |
2.24 % |
9444458 |
2.43 % |
836043 |
1.19 % |
| q20,qd2,mq40 |
7361728 |
1.60 % |
4924034 |
1.27 % |
2437694 |
3.47 % |
| qd2,mq40 |
205861 |
0.04 % |
166932 |
0.04 % |
38929 |
0.06 % |
| fs60 |
579 |
0.00 % |
0 |
0.00 % |
579 |
0.00 % |
| fs60,mq40 |
382 |
0.00 % |
0 |
0.00 % |
382 |
0.00 % |
| q20,qd2,fs60 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| q20,fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,qd2,fs60,mq40 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| qd2,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| qd2,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
22684346 |
24.78 % |
| Transition |
G>A |
All |
7759277 |
8.48 % |
| Transition |
T>C |
All |
29328302 |
32.04 % |
| Transition |
C>T |
All |
5848230 |
6.39 % |
| Transversion |
A>C |
All |
1955549 |
2.14 % |
| Transversion |
C>A |
All |
3365034 |
3.68 % |
| Transversion |
T>G |
All |
3314701 |
3.62 % |
| Transversion |
G>T |
All |
3000573 |
3.28 % |
| Transversion |
A>T |
All |
5187031 |
5.67 % |
| Transversion |
T>A |
All |
5716812 |
6.25 % |
| Transversion |
C>G |
All |
2004432 |
2.19 % |
| Transversion |
G>C |
All |
1367110 |
1.49 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1576746 |
20.68 % |
| Transition |
G>A |
Passed |
701451 |
9.20 % |
| Transition |
T>C |
Passed |
2748853 |
36.06 % |
| Transition |
C>T |
Passed |
458437 |
6.01 % |
| Transversion |
A>C |
Passed |
224873 |
2.95 % |
| Transversion |
C>A |
Passed |
284350 |
3.73 % |
| Transversion |
T>G |
Passed |
416941 |
5.47 % |
| Transversion |
G>T |
Passed |
154673 |
2.03 % |
| Transversion |
A>T |
Passed |
173214 |
2.27 % |
| Transversion |
T>A |
Passed |
391660 |
5.14 % |
| Transversion |
C>G |
Passed |
296186 |
3.88 % |
| Transversion |
G>C |
Passed |
196491 |
2.58 % |
| |
|
|
|
|
| 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 |
2.53 |
65620155 |
25911242 |
| Passed |
2.57 |
5485487 |
2138388 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |