/EXTERNAL CREST/variants/K006461_1_lane_gembs
BACK
SAMPLE K006461_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1240890666 |
618068964 |
49.81 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1240890666 |
100% |
1090251880 |
87.86 % |
150638786 |
12.14 % |
| |
|
|
|
|
|
|
| Passed |
638385939 |
51.45 % |
607549039 |
55.73 % |
30836900 |
4.83 % |
| Filtered |
602504727 |
48.55 % |
482702841 |
44.27 % |
119801886 |
18.77 % |
| |
|
|
|
|
|
|
| q20 |
379558864 |
63.00 % |
351664144 |
72.85 % |
27894720 |
23.28 % |
| q20,qd2 |
133538543 |
22.16 % |
51410085 |
10.65 % |
82128458 |
68.55 % |
| q20,mq40 |
46812078 |
7.77 % |
44465341 |
9.21 % |
2346737 |
1.96 % |
| mq40 |
19551362 |
3.25 % |
16918937 |
3.51 % |
2632425 |
2.20 % |
| qd2 |
13299591 |
2.21 % |
12224454 |
2.53 % |
1075137 |
0.90 % |
| q20,qd2,mq40 |
9592517 |
1.59 % |
5891014 |
1.22 % |
3701503 |
3.09 % |
| qd2,mq40 |
150489 |
0.02 % |
128866 |
0.03 % |
21623 |
0.02 % |
| fs60 |
678 |
0.00 % |
0 |
0.00 % |
678 |
0.00 % |
| fs60,mq40 |
525 |
0.00 % |
0 |
0.00 % |
525 |
0.00 % |
| q20,qd2,fs60 |
34 |
0.00 % |
0 |
0.00 % |
34 |
0.00 % |
| q20,fs60 |
23 |
0.00 % |
0 |
0.00 % |
23 |
0.00 % |
| qd2,fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| qd2,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
29684681 |
19.44 % |
| Transition |
G>A |
All |
10827745 |
7.09 % |
| Transition |
T>C |
All |
38999722 |
25.55 % |
| Transition |
C>T |
All |
8387655 |
5.49 % |
| Transversion |
A>C |
All |
3138706 |
2.06 % |
| Transversion |
C>A |
All |
12319473 |
8.07 % |
| Transversion |
T>G |
All |
4749074 |
3.11 % |
| Transversion |
G>T |
All |
13893591 |
9.10 % |
| Transversion |
A>T |
All |
9725429 |
6.37 % |
| Transversion |
T>A |
All |
10134225 |
6.64 % |
| Transversion |
C>G |
All |
5425611 |
3.55 % |
| Transversion |
G>C |
All |
5377231 |
3.52 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1949623 |
17.70 % |
| Transition |
G>A |
Passed |
807607 |
7.33 % |
| Transition |
T>C |
Passed |
3169902 |
28.77 % |
| Transition |
C>T |
Passed |
495255 |
4.50 % |
| Transversion |
A>C |
Passed |
314589 |
2.86 % |
| Transversion |
C>A |
Passed |
642124 |
5.83 % |
| Transversion |
T>G |
Passed |
542284 |
4.92 % |
| Transversion |
G>T |
Passed |
377982 |
3.43 % |
| Transversion |
A>T |
Passed |
274465 |
2.49 % |
| Transversion |
T>A |
Passed |
610805 |
5.54 % |
| Transversion |
C>G |
Passed |
904878 |
8.21 % |
| Transversion |
G>C |
Passed |
927129 |
8.42 % |
| |
|
|
|
|
| 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 |
1.36 |
87899803 |
64763340 |
| Passed |
1.40 |
6422387 |
4594256 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |