/EXTERNAL CREST/variants/K006478_1_lane_gembs
BACK
SAMPLE K006478_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1136701580 |
47944250 |
4.22 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1136701580 |
100% |
1080896297 |
95.09 % |
55805283 |
4.91 % |
| |
|
|
|
|
|
|
| Passed |
68206058 |
6.00 % |
46973848 |
4.35 % |
21232210 |
31.13 % |
| Filtered |
1068495522 |
94.00 % |
1033922449 |
95.65 % |
34573073 |
50.69 % |
| |
|
|
|
|
|
|
| q20 |
916075142 |
85.74 % |
900950173 |
87.14 % |
15124969 |
43.75 % |
| q20,qd2 |
71869928 |
6.73 % |
55136651 |
5.33 % |
16733277 |
48.40 % |
| q20,mq40 |
64040242 |
5.99 % |
63196671 |
6.11 % |
843571 |
2.44 % |
| q20,qd2,mq40 |
14123460 |
1.32 % |
13558947 |
1.31 % |
564513 |
1.63 % |
| mq40 |
2378335 |
0.22 % |
1073483 |
0.10 % |
1304852 |
3.77 % |
| qd2 |
4650 |
0.00 % |
3785 |
0.00 % |
865 |
0.00 % |
| qd2,mq40 |
3734 |
0.00 % |
2739 |
0.00 % |
995 |
0.00 % |
| fs60,mq40 |
27 |
0.00 % |
0 |
0.00 % |
27 |
0.00 % |
| qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,fs60,mq40 |
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 |
8986105 |
15.09 % |
| Transition |
G>A |
All |
3894660 |
6.54 % |
| Transition |
T>C |
All |
8776642 |
14.74 % |
| Transition |
C>T |
All |
2476702 |
4.16 % |
| Transversion |
A>C |
All |
1785609 |
3.00 % |
| Transversion |
C>A |
All |
5376232 |
9.03 % |
| Transversion |
T>G |
All |
3617073 |
6.07 % |
| Transversion |
G>T |
All |
5568255 |
9.35 % |
| Transversion |
A>T |
All |
7605611 |
12.77 % |
| Transversion |
T>A |
All |
7435374 |
12.48 % |
| Transversion |
C>G |
All |
2578955 |
4.33 % |
| Transversion |
G>C |
All |
1457680 |
2.45 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
164027 |
16.54 % |
| Transition |
G>A |
Passed |
112138 |
11.31 % |
| Transition |
T>C |
Passed |
159975 |
16.13 % |
| Transition |
C>T |
Passed |
68945 |
6.95 % |
| Transversion |
A>C |
Passed |
48251 |
4.87 % |
| Transversion |
C>A |
Passed |
67457 |
6.80 % |
| Transversion |
T>G |
Passed |
84640 |
8.53 % |
| Transversion |
G>T |
Passed |
46547 |
4.69 % |
| Transversion |
A>T |
Passed |
42474 |
4.28 % |
| Transversion |
T>A |
Passed |
76849 |
7.75 % |
| Transversion |
C>G |
Passed |
71030 |
7.16 % |
| Transversion |
G>C |
Passed |
49419 |
4.98 % |
| |
|
|
|
|
| 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 |
0.68 |
24134109 |
35424789 |
| Passed |
1.04 |
505085 |
486667 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |