/EXTERNAL CREST/variants/K006460_1_lane_gembs
BACK
SAMPLE K006460_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1235339057 |
664947307 |
53.83 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1235339057 |
100% |
1101917754 |
89.20 % |
133421303 |
10.80 % |
| |
|
|
|
|
|
|
| Passed |
683162856 |
55.30 % |
655271951 |
59.47 % |
27890905 |
4.08 % |
| Filtered |
552176201 |
44.70 % |
446645803 |
40.53 % |
105530398 |
15.45 % |
| |
|
|
|
|
|
|
| q20 |
349894150 |
63.37 % |
324787472 |
72.72 % |
25106678 |
23.79 % |
| q20,qd2 |
114524902 |
20.74 % |
42913518 |
9.61 % |
71611384 |
67.86 % |
| q20,mq40 |
43868623 |
7.94 % |
41756833 |
9.35 % |
2111790 |
2.00 % |
| mq40 |
21181056 |
3.84 % |
18826388 |
4.22 % |
2354668 |
2.23 % |
| qd2 |
13853646 |
2.51 % |
12742028 |
2.85 % |
1111618 |
1.05 % |
| q20,qd2,mq40 |
8685175 |
1.57 % |
5475777 |
1.23 % |
3209398 |
3.04 % |
| qd2,mq40 |
167310 |
0.03 % |
143787 |
0.03 % |
23523 |
0.02 % |
| fs60 |
761 |
0.00 % |
0 |
0.00 % |
761 |
0.00 % |
| fs60,mq40 |
475 |
0.00 % |
0 |
0.00 % |
475 |
0.00 % |
| q20,qd2,fs60 |
52 |
0.00 % |
0 |
0.00 % |
52 |
0.00 % |
| q20,fs60 |
32 |
0.00 % |
0 |
0.00 % |
32 |
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,qd2,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
28283391 |
20.89 % |
| Transition |
G>A |
All |
10088293 |
7.45 % |
| Transition |
T>C |
All |
37747256 |
27.88 % |
| Transition |
C>T |
All |
7741011 |
5.72 % |
| Transversion |
A>C |
All |
2875024 |
2.12 % |
| Transversion |
C>A |
All |
9135362 |
6.75 % |
| Transversion |
T>G |
All |
4337744 |
3.20 % |
| Transversion |
G>T |
All |
9864884 |
7.29 % |
| Transversion |
A>T |
All |
8540916 |
6.31 % |
| Transversion |
T>A |
All |
8894812 |
6.57 % |
| Transversion |
C>G |
All |
4136477 |
3.05 % |
| Transversion |
G>C |
All |
3763695 |
2.78 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1934261 |
18.92 % |
| Transition |
G>A |
Passed |
805470 |
7.88 % |
| Transition |
T>C |
Passed |
3280384 |
32.09 % |
| Transition |
C>T |
Passed |
505305 |
4.94 % |
| Transversion |
A>C |
Passed |
309774 |
3.03 % |
| Transversion |
C>A |
Passed |
524085 |
5.13 % |
| Transversion |
T>G |
Passed |
513668 |
5.03 % |
| Transversion |
G>T |
Passed |
297186 |
2.91 % |
| Transversion |
A>T |
Passed |
254500 |
2.49 % |
| Transversion |
T>A |
Passed |
566847 |
5.55 % |
| Transversion |
C>G |
Passed |
643286 |
6.29 % |
| Transversion |
G>C |
Passed |
586135 |
5.73 % |
| |
|
|
|
|
| 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 |
1.63 |
83859951 |
51548914 |
| Passed |
1.77 |
6525420 |
3695481 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |