/EXTERNAL CREST/variants/K006440_1_lane_gembs
BACK
SAMPLE K006440_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1198721520 |
575321847 |
47.99 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1198721520 |
100% |
1109882643 |
92.59 % |
88838877 |
7.41 % |
| |
|
|
|
|
|
|
| Passed |
595576396 |
49.68 % |
570303788 |
51.38 % |
25272608 |
4.24 % |
| Filtered |
603145124 |
50.32 % |
539578855 |
48.62 % |
63566269 |
10.67 % |
| |
|
|
|
|
|
|
| q20 |
496798106 |
82.37 % |
475133853 |
88.06 % |
21664253 |
34.08 % |
| q20,qd2 |
69577564 |
11.54 % |
30184816 |
5.59 % |
39392748 |
61.97 % |
| q20,mq40 |
17102215 |
2.84 % |
16519661 |
3.06 % |
582554 |
0.92 % |
| qd2 |
10778509 |
1.79 % |
10136676 |
1.88 % |
641833 |
1.01 % |
| q20,qd2,mq40 |
5901862 |
0.98 % |
5362754 |
0.99 % |
539108 |
0.85 % |
| mq40 |
2934561 |
0.49 % |
2200710 |
0.41 % |
733851 |
1.15 % |
| qd2,mq40 |
50963 |
0.01 % |
40385 |
0.01 % |
10578 |
0.02 % |
| q20,qd2,fs60 |
635 |
0.00 % |
0 |
0.00 % |
635 |
0.00 % |
| fs60 |
249 |
0.00 % |
0 |
0.00 % |
249 |
0.00 % |
| qd2,fs60,mq40 |
148 |
0.00 % |
0 |
0.00 % |
148 |
0.00 % |
| fs60,mq40 |
132 |
0.00 % |
0 |
0.00 % |
132 |
0.00 % |
| qd2,fs60 |
116 |
0.00 % |
0 |
0.00 % |
116 |
0.00 % |
| q20,qd2,fs60,mq40 |
60 |
0.00 % |
0 |
0.00 % |
60 |
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 |
20085527 |
21.81 % |
| Transition |
G>A |
All |
6835158 |
7.42 % |
| Transition |
T>C |
All |
23031383 |
25.00 % |
| Transition |
C>T |
All |
5133012 |
5.57 % |
| Transversion |
A>C |
All |
3298853 |
3.58 % |
| Transversion |
C>A |
All |
4921341 |
5.34 % |
| Transversion |
T>G |
All |
4283590 |
4.65 % |
| Transversion |
G>T |
All |
4483785 |
4.87 % |
| Transversion |
A>T |
All |
7319468 |
7.95 % |
| Transversion |
T>A |
All |
8307725 |
9.02 % |
| Transversion |
C>G |
All |
2418882 |
2.63 % |
| Transversion |
G>C |
All |
1989922 |
2.16 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1007862 |
18.35 % |
| Transition |
G>A |
Passed |
548741 |
9.99 % |
| Transition |
T>C |
Passed |
1509311 |
27.48 % |
| Transition |
C>T |
Passed |
444040 |
8.08 % |
| Transversion |
A>C |
Passed |
259245 |
4.72 % |
| Transversion |
C>A |
Passed |
257136 |
4.68 % |
| Transversion |
T>G |
Passed |
333304 |
6.07 % |
| Transversion |
G>T |
Passed |
169437 |
3.08 % |
| Transversion |
A>T |
Passed |
178070 |
3.24 % |
| Transversion |
T>A |
Passed |
326348 |
5.94 % |
| Transversion |
C>G |
Passed |
252296 |
4.59 % |
| Transversion |
G>C |
Passed |
206817 |
3.77 % |
| |
|
|
|
|
| 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 |
1.49 |
55085080 |
37023566 |
| Passed |
1.77 |
3509954 |
1982653 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |