/EXTERNAL BLUEPRINT/variants/K011725_1_lane_gembs
BACK
SAMPLE K011725_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
655888481 |
495610 |
0.08 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
655888481 |
100% |
648630683 |
98.89 % |
7257798 |
1.11 % |
| |
|
|
|
|
|
|
| Passed |
4111567 |
0.63 % |
401441 |
0.06 % |
3710126 |
90.24 % |
| Filtered |
651776914 |
99.37 % |
648229242 |
99.94 % |
3547672 |
86.29 % |
| |
|
|
|
|
|
|
| q20 |
426748164 |
65.47 % |
423941707 |
65.40 % |
2806457 |
79.11 % |
| q20,qd2 |
167705342 |
25.73 % |
167369342 |
25.82 % |
336000 |
9.47 % |
| q20,mq40 |
36159517 |
5.55 % |
35984067 |
5.55 % |
175450 |
4.95 % |
| q20,qd2,mq40 |
20932850 |
3.21 % |
20907547 |
3.23 % |
25303 |
0.71 % |
| mq40 |
226069 |
0.03 % |
21787 |
0.00 % |
204282 |
5.76 % |
| qd2 |
4339 |
0.00 % |
4281 |
0.00 % |
58 |
0.00 % |
| qd2,mq40 |
595 |
0.00 % |
511 |
0.00 % |
84 |
0.00 % |
| qd2,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
2688139 |
23.20 % |
| Transition |
G>A |
All |
923937 |
7.97 % |
| Transition |
T>C |
All |
3505760 |
30.25 % |
| Transition |
C>T |
All |
454700 |
3.92 % |
| Transversion |
A>C |
All |
434274 |
3.75 % |
| Transversion |
C>A |
All |
601079 |
5.19 % |
| Transversion |
T>G |
All |
537035 |
4.63 % |
| Transversion |
G>T |
All |
546851 |
4.72 % |
| Transversion |
A>T |
All |
455642 |
3.93 % |
| Transversion |
T>A |
All |
629849 |
5.44 % |
| Transversion |
C>G |
All |
373257 |
3.22 % |
| Transversion |
G>C |
All |
437717 |
3.78 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
14175 |
15.38 % |
| Transition |
G>A |
Passed |
14334 |
15.55 % |
| Transition |
T>C |
Passed |
24464 |
26.54 % |
| Transition |
C>T |
Passed |
6336 |
6.87 % |
| Transversion |
A>C |
Passed |
3859 |
4.19 % |
| Transversion |
C>A |
Passed |
5061 |
5.49 % |
| Transversion |
T>G |
Passed |
4073 |
4.42 % |
| Transversion |
G>T |
Passed |
2901 |
3.15 % |
| Transversion |
A>T |
Passed |
1888 |
2.05 % |
| Transversion |
T>A |
Passed |
4323 |
4.69 % |
| Transversion |
C>G |
Passed |
4232 |
4.59 % |
| Transversion |
G>C |
Passed |
6542 |
7.10 % |
| |
|
|
|
|
| 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 |
1.89 |
7572536 |
4015704 |
| Passed |
1.80 |
59309 |
32879 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |