/EXTERNAL CREST/variants/K006432_1_lane_gembs
BACK
SAMPLE K006432_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1211299490 |
854948906 |
70.58 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1211299490 |
100% |
1129552364 |
93.25 % |
81747126 |
6.75 % |
| |
|
|
|
|
|
|
| Passed |
864030864 |
71.33 % |
846992231 |
74.98 % |
17038633 |
1.97 % |
| Filtered |
347268626 |
28.67 % |
282560133 |
25.02 % |
64708493 |
7.49 % |
| |
|
|
|
|
|
|
| q20 |
186104640 |
53.59 % |
172272397 |
60.97 % |
13832243 |
21.38 % |
| q20,qd2 |
64912454 |
18.69 % |
21800078 |
7.72 % |
43112376 |
66.63 % |
| mq40 |
35093015 |
10.11 % |
33169111 |
11.74 % |
1923904 |
2.97 % |
| q20,mq40 |
33346672 |
9.60 % |
31729147 |
11.23 % |
1617525 |
2.50 % |
| qd2 |
20559921 |
5.92 % |
19037918 |
6.74 % |
1522003 |
2.35 % |
| q20,qd2,mq40 |
6784010 |
1.95 % |
4170082 |
1.48 % |
2613928 |
4.04 % |
| qd2,mq40 |
465164 |
0.13 % |
381400 |
0.13 % |
83764 |
0.13 % |
| fs60 |
1643 |
0.00 % |
0 |
0.00 % |
1643 |
0.00 % |
| fs60,mq40 |
881 |
0.00 % |
0 |
0.00 % |
881 |
0.00 % |
| q20,qd2,fs60 |
118 |
0.00 % |
0 |
0.00 % |
118 |
0.00 % |
| q20,fs60 |
47 |
0.00 % |
0 |
0.00 % |
47 |
0.00 % |
| q20,qd2,fs60,mq40 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| qd2,fs60 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| q20,fs60,mq40 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| qd2,fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
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 |
21726398 |
26.02 % |
| Transition |
G>A |
All |
7296295 |
8.74 % |
| Transition |
T>C |
All |
28647966 |
34.31 % |
| Transition |
C>T |
All |
6392795 |
7.66 % |
| Transversion |
A>C |
All |
1487182 |
1.78 % |
| Transversion |
C>A |
All |
2466226 |
2.95 % |
| Transversion |
T>G |
All |
2401331 |
2.88 % |
| Transversion |
G>T |
All |
2265962 |
2.71 % |
| Transversion |
A>T |
All |
4034241 |
4.83 % |
| Transversion |
T>A |
All |
4353830 |
5.21 % |
| Transversion |
C>G |
All |
1419749 |
1.70 % |
| Transversion |
G>C |
All |
1012908 |
1.21 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1944094 |
22.26 % |
| Transition |
G>A |
Passed |
797987 |
9.14 % |
| Transition |
T>C |
Passed |
3318692 |
38.00 % |
| Transition |
C>T |
Passed |
596779 |
6.83 % |
| Transversion |
A>C |
Passed |
229997 |
2.63 % |
| Transversion |
C>A |
Passed |
265026 |
3.03 % |
| Transversion |
T>G |
Passed |
374794 |
4.29 % |
| Transversion |
G>T |
Passed |
171959 |
1.97 % |
| Transversion |
A>T |
Passed |
201126 |
2.30 % |
| Transversion |
T>A |
Passed |
369084 |
4.23 % |
| Transversion |
C>G |
Passed |
267037 |
3.06 % |
| Transversion |
G>C |
Passed |
196769 |
2.25 % |
| |
|
|
|
|
| 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 |
3.30 |
64063454 |
19441429 |
| Passed |
3.21 |
6657552 |
2075792 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |