/EXTERNAL CREST/variants/K006444_1_lane_gembs
BACK
SAMPLE K006444_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1176833657 |
441582798 |
37.52 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1176833657 |
100% |
1096077074 |
93.14 % |
80756583 |
6.86 % |
| |
|
|
|
|
|
|
| Passed |
462574588 |
39.31 % |
437757997 |
39.94 % |
24816591 |
5.36 % |
| Filtered |
714259069 |
60.69 % |
658319077 |
60.06 % |
55939992 |
12.09 % |
| |
|
|
|
|
|
|
| q20 |
603921616 |
84.55 % |
584542580 |
88.79 % |
19379036 |
34.64 % |
| q20,qd2 |
74610787 |
10.45 % |
40047897 |
6.08 % |
34562890 |
61.79 % |
| q20,mq40 |
18460795 |
2.58 % |
17988131 |
2.73 % |
472664 |
0.84 % |
| qd2 |
8000514 |
1.12 % |
7602225 |
1.15 % |
398289 |
0.71 % |
| q20,qd2,mq40 |
7146578 |
1.00 % |
6704079 |
1.02 % |
442499 |
0.79 % |
| mq40 |
2073442 |
0.29 % |
1400338 |
0.21 % |
673104 |
1.20 % |
| qd2,mq40 |
43331 |
0.01 % |
33827 |
0.01 % |
9504 |
0.02 % |
| q20,qd2,fs60 |
1057 |
0.00 % |
0 |
0.00 % |
1057 |
0.00 % |
| fs60 |
299 |
0.00 % |
0 |
0.00 % |
299 |
0.00 % |
| qd2,fs60 |
188 |
0.00 % |
0 |
0.00 % |
188 |
0.00 % |
| qd2,fs60,mq40 |
182 |
0.00 % |
0 |
0.00 % |
182 |
0.00 % |
| fs60,mq40 |
163 |
0.00 % |
0 |
0.00 % |
163 |
0.00 % |
| q20,qd2,fs60,mq40 |
113 |
0.00 % |
0 |
0.00 % |
113 |
0.00 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,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 |
16911365 |
20.00 % |
| Transition |
G>A |
All |
5583584 |
6.60 % |
| Transition |
T>C |
All |
18282386 |
21.62 % |
| Transition |
C>T |
All |
4651525 |
5.50 % |
| Transversion |
A>C |
All |
2928233 |
3.46 % |
| Transversion |
C>A |
All |
5774226 |
6.83 % |
| Transversion |
T>G |
All |
3640557 |
4.31 % |
| Transversion |
G>T |
All |
5651627 |
6.68 % |
| Transversion |
A>T |
All |
7902178 |
9.35 % |
| Transversion |
T>A |
All |
8293200 |
9.81 % |
| Transversion |
C>G |
All |
2624624 |
3.10 % |
| Transversion |
G>C |
All |
2300702 |
2.72 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
725535 |
17.25 % |
| Transition |
G>A |
Passed |
423692 |
10.07 % |
| Transition |
T>C |
Passed |
1004555 |
23.88 % |
| Transition |
C>T |
Passed |
384992 |
9.15 % |
| Transversion |
A>C |
Passed |
232890 |
5.54 % |
| Transversion |
C>A |
Passed |
204769 |
4.87 % |
| Transversion |
T>G |
Passed |
241817 |
5.75 % |
| Transversion |
G>T |
Passed |
173685 |
4.13 % |
| Transversion |
A>T |
Passed |
164227 |
3.90 % |
| Transversion |
T>A |
Passed |
226751 |
5.39 % |
| Transversion |
C>G |
Passed |
218545 |
5.19 % |
| Transversion |
G>C |
Passed |
205480 |
4.88 % |
| |
|
|
|
|
| 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 |
1.16 |
45428860 |
39115347 |
| Passed |
1.52 |
2538774 |
1668164 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |