/EXTERNAL CREST/variants/K006453_1_lane_gembs
BACK
SAMPLE K006453_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1224754962 |
717138845 |
58.55 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1224754962 |
100% |
1111332330 |
90.74 % |
113422632 |
9.26 % |
| |
|
|
|
|
|
|
| Passed |
733475766 |
59.89 % |
709088216 |
63.81 % |
24387550 |
3.32 % |
| Filtered |
491279196 |
40.11 % |
402244114 |
36.19 % |
89035082 |
12.14 % |
| |
|
|
|
|
|
|
| q20 |
318142772 |
64.76 % |
297321038 |
73.92 % |
20821734 |
23.39 % |
| q20,qd2 |
91313384 |
18.59 % |
30401315 |
7.56 % |
60912069 |
68.41 % |
| q20,mq40 |
39854734 |
8.11 % |
38128956 |
9.48 % |
1725778 |
1.94 % |
| mq40 |
24217093 |
4.93 % |
22237218 |
5.53 % |
1979875 |
2.22 % |
| qd2 |
10094408 |
2.05 % |
9116473 |
2.27 % |
977935 |
1.10 % |
| q20,qd2,mq40 |
7506305 |
1.53 % |
4916913 |
1.22 % |
2589392 |
2.91 % |
| qd2,mq40 |
149671 |
0.03 % |
122201 |
0.03 % |
27470 |
0.03 % |
| fs60 |
481 |
0.00 % |
0 |
0.00 % |
481 |
0.00 % |
| fs60,mq40 |
267 |
0.00 % |
0 |
0.00 % |
267 |
0.00 % |
| q20,qd2,fs60 |
46 |
0.00 % |
0 |
0.00 % |
46 |
0.00 % |
| q20,fs60 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| qd2,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 % |
| q20,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
28354251 |
24.56 % |
| Transition |
G>A |
All |
10118040 |
8.76 % |
| Transition |
T>C |
All |
34184906 |
29.61 % |
| Transition |
C>T |
All |
7011747 |
6.07 % |
| Transversion |
A>C |
All |
2392734 |
2.07 % |
| Transversion |
C>A |
All |
5145864 |
4.46 % |
| Transversion |
T>G |
All |
3819126 |
3.31 % |
| Transversion |
G>T |
All |
4831673 |
4.19 % |
| Transversion |
A>T |
All |
7354467 |
6.37 % |
| Transversion |
T>A |
All |
7878062 |
6.82 % |
| Transversion |
C>G |
All |
2520812 |
2.18 % |
| Transversion |
G>C |
All |
1837308 |
1.59 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1859125 |
21.44 % |
| Transition |
G>A |
Passed |
794241 |
9.16 % |
| Transition |
T>C |
Passed |
2862778 |
33.01 % |
| Transition |
C>T |
Passed |
497456 |
5.74 % |
| Transversion |
A>C |
Passed |
276380 |
3.19 % |
| Transversion |
C>A |
Passed |
374324 |
4.32 % |
| Transversion |
T>G |
Passed |
453974 |
5.24 % |
| Transversion |
G>T |
Passed |
203735 |
2.35 % |
| Transversion |
A>T |
Passed |
230595 |
2.66 % |
| Transversion |
T>A |
Passed |
505717 |
5.83 % |
| Transversion |
C>G |
Passed |
353802 |
4.08 % |
| Transversion |
G>C |
Passed |
259285 |
2.99 % |
| |
|
|
|
|
| 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 |
2.23 |
79668944 |
35780046 |
| Passed |
2.26 |
6013600 |
2657812 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |