/EXTERNAL BLUEPRINT/variants/K006361_10_lane_gembs
BACK
SAMPLE K006361_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1133630855 |
692542366 |
61.09 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1133630855 |
100% |
1120413855 |
98.83 % |
13217000 |
1.17 % |
| |
|
|
|
|
|
|
| Passed |
694514732 |
61.26 % |
691023026 |
61.68 % |
3491706 |
0.50 % |
| Filtered |
439116123 |
38.74 % |
429390829 |
38.32 % |
9725294 |
1.40 % |
| |
|
|
|
|
|
|
| q20 |
380338092 |
86.61 % |
378492200 |
88.15 % |
1845892 |
18.98 % |
| q20,qd2 |
32550268 |
7.41 % |
25250332 |
5.88 % |
7299936 |
75.06 % |
| q20,mq40 |
13723865 |
3.13 % |
13616295 |
3.17 % |
107570 |
1.11 % |
| mq40 |
5779369 |
1.32 % |
5617617 |
1.31 % |
161752 |
1.66 % |
| qd2 |
3493868 |
0.80 % |
3406171 |
0.79 % |
87697 |
0.90 % |
| q20,qd2,mq40 |
3155223 |
0.72 % |
2946722 |
0.69 % |
208501 |
2.14 % |
| qd2,mq40 |
70900 |
0.02 % |
61492 |
0.01 % |
9408 |
0.10 % |
| q20,qd2,fs60 |
1458 |
0.00 % |
0 |
0.00 % |
1458 |
0.01 % |
| fs60 |
936 |
0.00 % |
0 |
0.00 % |
936 |
0.01 % |
| qd2,fs60,mq40 |
837 |
0.00 % |
0 |
0.00 % |
837 |
0.01 % |
| qd2,fs60 |
569 |
0.00 % |
0 |
0.00 % |
569 |
0.01 % |
| fs60,mq40 |
374 |
0.00 % |
0 |
0.00 % |
374 |
0.00 % |
| q20,qd2,fs60,mq40 |
361 |
0.00 % |
0 |
0.00 % |
361 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
3633486 |
23.82 % |
| Transition |
G>A |
All |
2327440 |
15.26 % |
| Transition |
T>C |
All |
3264921 |
21.41 % |
| Transition |
C>T |
All |
2220913 |
14.56 % |
| Transversion |
A>C |
All |
248177 |
1.63 % |
| Transversion |
C>A |
All |
829942 |
5.44 % |
| Transversion |
T>G |
All |
278514 |
1.83 % |
| Transversion |
G>T |
All |
805906 |
5.28 % |
| Transversion |
A>T |
All |
599603 |
3.93 % |
| Transversion |
T>A |
All |
608528 |
3.99 % |
| Transversion |
C>G |
All |
224886 |
1.47 % |
| Transversion |
G>C |
All |
210404 |
1.38 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
409237 |
18.37 % |
| Transition |
G>A |
Passed |
374259 |
16.80 % |
| Transition |
T>C |
Passed |
406509 |
18.25 % |
| Transition |
C>T |
Passed |
373957 |
16.79 % |
| Transversion |
A>C |
Passed |
89306 |
4.01 % |
| Transversion |
C>A |
Passed |
81806 |
3.67 % |
| Transversion |
T>G |
Passed |
88844 |
3.99 % |
| Transversion |
G>T |
Passed |
82334 |
3.70 % |
| Transversion |
A>T |
Passed |
59057 |
2.65 % |
| Transversion |
T>A |
Passed |
58665 |
2.63 % |
| Transversion |
C>G |
Passed |
101452 |
4.55 % |
| Transversion |
G>C |
Passed |
102251 |
4.59 % |
| |
|
|
|
|
| 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 |
3.01 |
11446760 |
3805960 |
| Passed |
2.36 |
1563962 |
663715 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |