/EXTERNAL BLUEPRINT/variants/K006284_14_lane_gembs
BACK
SAMPLE K006284_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1131695895 |
664267725 |
58.70 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1131695895 |
100% |
1120167943 |
98.98 % |
11527952 |
1.02 % |
| |
|
|
|
|
|
|
| Passed |
666723445 |
58.91 % |
662701245 |
59.16 % |
4022200 |
0.60 % |
| Filtered |
464972450 |
41.09 % |
457466698 |
40.84 % |
7505752 |
1.13 % |
| |
|
|
|
|
|
|
| q20 |
418855011 |
90.08 % |
417178056 |
91.19 % |
1676955 |
22.34 % |
| q20,qd2 |
20933703 |
4.50 % |
15688751 |
3.43 % |
5244952 |
69.88 % |
| q20,mq40 |
14267034 |
3.07 % |
14164066 |
3.10 % |
102968 |
1.37 % |
| mq40 |
6029503 |
1.30 % |
5836142 |
1.28 % |
193361 |
2.58 % |
| q20,qd2,mq40 |
2732360 |
0.59 % |
2563317 |
0.56 % |
169043 |
2.25 % |
| qd2 |
2079932 |
0.45 % |
1976240 |
0.43 % |
103692 |
1.38 % |
| qd2,mq40 |
70533 |
0.02 % |
60126 |
0.01 % |
10407 |
0.14 % |
| qd2,fs60,mq40 |
1169 |
0.00 % |
0 |
0.00 % |
1169 |
0.02 % |
| fs60 |
963 |
0.00 % |
0 |
0.00 % |
963 |
0.01 % |
| qd2,fs60 |
771 |
0.00 % |
0 |
0.00 % |
771 |
0.01 % |
| q20,qd2,fs60 |
752 |
0.00 % |
0 |
0.00 % |
752 |
0.01 % |
| fs60,mq40 |
510 |
0.00 % |
0 |
0.00 % |
510 |
0.01 % |
| q20,qd2,fs60,mq40 |
208 |
0.00 % |
0 |
0.00 % |
208 |
0.00 % |
| q20,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 |
3961807 |
29.44 % |
| Transition |
G>A |
All |
1430198 |
10.63 % |
| Transition |
T>C |
All |
3844089 |
28.56 % |
| Transition |
C>T |
All |
1406460 |
10.45 % |
| Transversion |
A>C |
All |
218865 |
1.63 % |
| Transversion |
C>A |
All |
590850 |
4.39 % |
| Transversion |
T>G |
All |
226737 |
1.68 % |
| Transversion |
G>T |
All |
579406 |
4.31 % |
| Transversion |
A>T |
All |
391400 |
2.91 % |
| Transversion |
T>A |
All |
384561 |
2.86 % |
| Transversion |
C>G |
All |
214440 |
1.59 % |
| Transversion |
G>C |
All |
209290 |
1.56 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
411875 |
18.41 % |
| Transition |
G>A |
Passed |
367075 |
16.41 % |
| Transition |
T>C |
Passed |
410495 |
18.35 % |
| Transition |
C>T |
Passed |
367910 |
16.44 % |
| Transversion |
A>C |
Passed |
88887 |
3.97 % |
| Transversion |
C>A |
Passed |
84367 |
3.77 % |
| Transversion |
T>G |
Passed |
88458 |
3.95 % |
| Transversion |
G>T |
Passed |
84227 |
3.76 % |
| Transversion |
A>T |
Passed |
59913 |
2.68 % |
| Transversion |
T>A |
Passed |
59783 |
2.67 % |
| Transversion |
C>G |
Passed |
106797 |
4.77 % |
| Transversion |
G>C |
Passed |
107433 |
4.80 % |
| |
|
|
|
|
| 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 |
3.78 |
10642554 |
2815549 |
| Passed |
2.29 |
1557355 |
679865 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |