/EXTERNAL CREST/variants/K006456_1_lane_gembs
BACK
SAMPLE K006456_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1220103011 |
777924049 |
63.76 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1220103011 |
100% |
1114546752 |
91.35 % |
105556259 |
8.65 % |
| |
|
|
|
|
|
|
| Passed |
791661842 |
64.88 % |
769475389 |
69.04 % |
22186453 |
2.80 % |
| Filtered |
428441169 |
35.12 % |
345071363 |
30.96 % |
83369806 |
10.53 % |
| |
|
|
|
|
|
|
| q20 |
254469684 |
59.39 % |
236605438 |
68.57 % |
17864246 |
21.43 % |
| q20,qd2 |
87522408 |
20.43 % |
29730366 |
8.62 % |
57792042 |
69.32 % |
| q20,mq40 |
37415455 |
8.73 % |
35732126 |
10.35 % |
1683329 |
2.02 % |
| mq40 |
26350584 |
6.15 % |
24371200 |
7.06 % |
1979384 |
2.37 % |
| qd2 |
15134361 |
3.53 % |
13765511 |
3.99 % |
1368850 |
1.64 % |
| q20,qd2,mq40 |
7335256 |
1.71 % |
4690426 |
1.36 % |
2644830 |
3.17 % |
| qd2,mq40 |
212178 |
0.05 % |
176296 |
0.05 % |
35882 |
0.04 % |
| fs60 |
695 |
0.00 % |
0 |
0.00 % |
695 |
0.00 % |
| fs60,mq40 |
418 |
0.00 % |
0 |
0.00 % |
418 |
0.00 % |
| q20,qd2,fs60 |
79 |
0.00 % |
0 |
0.00 % |
79 |
0.00 % |
| q20,fs60 |
41 |
0.00 % |
0 |
0.00 % |
41 |
0.00 % |
| qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
27253717 |
25.36 % |
| Transition |
G>A |
All |
9564216 |
8.90 % |
| Transition |
T>C |
All |
33800509 |
31.45 % |
| Transition |
C>T |
All |
6983313 |
6.50 % |
| Transversion |
A>C |
All |
2001978 |
1.86 % |
| Transversion |
C>A |
All |
4360669 |
4.06 % |
| Transversion |
T>G |
All |
3144917 |
2.93 % |
| Transversion |
G>T |
All |
4129453 |
3.84 % |
| Transversion |
A>T |
All |
6064512 |
5.64 % |
| Transversion |
T>A |
All |
6465759 |
6.02 % |
| Transversion |
C>G |
All |
2124300 |
1.98 % |
| Transversion |
G>C |
All |
1572117 |
1.46 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2006489 |
21.94 % |
| Transition |
G>A |
Passed |
840065 |
9.19 % |
| Transition |
T>C |
Passed |
3184485 |
34.83 % |
| Transition |
C>T |
Passed |
548948 |
6.00 % |
| Transversion |
A>C |
Passed |
269162 |
2.94 % |
| Transversion |
C>A |
Passed |
357371 |
3.91 % |
| Transversion |
T>G |
Passed |
429073 |
4.69 % |
| Transversion |
G>T |
Passed |
205410 |
2.25 % |
| Transversion |
A>T |
Passed |
231111 |
2.53 % |
| Transversion |
T>A |
Passed |
479262 |
5.24 % |
| Transversion |
C>G |
Passed |
338324 |
3.70 % |
| Transversion |
G>C |
Passed |
254145 |
2.78 % |
| |
|
|
|
|
| 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 |
2.60 |
77601755 |
29863705 |
| Passed |
2.57 |
6579987 |
2563858 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |