/EXTERNAL BLUEPRINT/variants/K010523_1_lane_gembs
BACK
SAMPLE K010523_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1108455291 |
278500705 |
25.13 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1108455291 |
100% |
1081627884 |
97.58 % |
26827407 |
2.42 % |
| |
|
|
|
|
|
|
| Passed |
285897812 |
25.79 % |
277316592 |
25.64 % |
8581220 |
3.00 % |
| Filtered |
822557479 |
74.21 % |
804311292 |
74.36 % |
18246187 |
6.38 % |
| |
|
|
|
|
|
|
| q20 |
745519507 |
90.63 % |
738789316 |
91.85 % |
6730191 |
36.89 % |
| q20,qd2 |
59049030 |
7.18 % |
47837668 |
5.95 % |
11211362 |
61.44 % |
| q20,mq40 |
12146122 |
1.48 % |
12052638 |
1.50 % |
93484 |
0.51 % |
| q20,qd2,mq40 |
5175604 |
0.63 % |
5106170 |
0.63 % |
69434 |
0.38 % |
| mq40 |
418752 |
0.05 % |
304631 |
0.04 % |
114121 |
0.63 % |
| qd2 |
231835 |
0.03 % |
207447 |
0.03 % |
24388 |
0.13 % |
| qd2,mq40 |
16179 |
0.00 % |
13422 |
0.00 % |
2757 |
0.02 % |
| qd2,fs60,mq40 |
236 |
0.00 % |
0 |
0.00 % |
236 |
0.00 % |
| fs60,mq40 |
82 |
0.00 % |
0 |
0.00 % |
82 |
0.00 % |
| qd2,fs60 |
69 |
0.00 % |
0 |
0.00 % |
69 |
0.00 % |
| q20,qd2,fs60,mq40 |
46 |
0.00 % |
0 |
0.00 % |
46 |
0.00 % |
| fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,qd2,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
9124469 |
31.64 % |
| Transition |
G>A |
All |
1284697 |
4.45 % |
| Transition |
T>C |
All |
9156718 |
31.75 % |
| Transition |
C>T |
All |
1285591 |
4.46 % |
| Transversion |
A>C |
All |
415430 |
1.44 % |
| Transversion |
C>A |
All |
1428851 |
4.95 % |
| Transversion |
T>G |
All |
413432 |
1.43 % |
| Transversion |
G>T |
All |
1418774 |
4.92 % |
| Transversion |
A>T |
All |
1833999 |
6.36 % |
| Transversion |
T>A |
All |
1842581 |
6.39 % |
| Transversion |
C>G |
All |
316468 |
1.10 % |
| Transversion |
G>C |
All |
318490 |
1.10 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
287073 |
19.30 % |
| Transition |
G>A |
Passed |
215463 |
14.48 % |
| Transition |
T>C |
Passed |
287157 |
19.30 % |
| Transition |
C>T |
Passed |
217207 |
14.60 % |
| Transversion |
A>C |
Passed |
59182 |
3.98 % |
| Transversion |
C>A |
Passed |
64682 |
4.35 % |
| Transversion |
T>G |
Passed |
59326 |
3.99 % |
| Transversion |
G>T |
Passed |
64312 |
4.32 % |
| Transversion |
A>T |
Passed |
60297 |
4.05 % |
| Transversion |
T>A |
Passed |
61483 |
4.13 % |
| Transversion |
C>G |
Passed |
55746 |
3.75 % |
| Transversion |
G>C |
Passed |
55727 |
3.75 % |
| |
|
|
|
|
| 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 |
2.61 |
20851475 |
7988025 |
| Passed |
2.09 |
1006900 |
480755 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |