/EXTERNAL BLUEPRINT/variants/K006379_15_lane_gembs
BACK
SAMPLE K006379_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1150517154 |
1067479343 |
92.78 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1150517154 |
100% |
1141170702 |
99.19 % |
9346452 |
0.81 % |
| |
|
|
|
|
|
|
| Passed |
1068073647 |
92.83 % |
1065265621 |
93.35 % |
2808026 |
0.26 % |
| Filtered |
82443507 |
7.17 % |
75905081 |
6.65 % |
6538426 |
0.61 % |
| |
|
|
|
|
|
|
| q20 |
52239422 |
63.36 % |
51743549 |
68.17 % |
495873 |
7.58 % |
| q20,mq40 |
12155227 |
14.74 % |
12055644 |
15.88 % |
99583 |
1.52 % |
| q20,qd2 |
8812413 |
10.69 % |
3413604 |
4.50 % |
5398809 |
82.57 % |
| mq40 |
4401250 |
5.34 % |
4200831 |
5.53 % |
200419 |
3.07 % |
| q20,qd2,mq40 |
3029012 |
3.67 % |
2854966 |
3.76 % |
174046 |
2.66 % |
| qd2 |
1753449 |
2.13 % |
1595287 |
2.10 % |
158162 |
2.42 % |
| qd2,mq40 |
51135 |
0.06 % |
41200 |
0.05 % |
9935 |
0.15 % |
| qd2,fs60,mq40 |
668 |
0.00 % |
0 |
0.00 % |
668 |
0.01 % |
| fs60,mq40 |
328 |
0.00 % |
0 |
0.00 % |
328 |
0.01 % |
| fs60 |
221 |
0.00 % |
0 |
0.00 % |
221 |
0.00 % |
| qd2,fs60 |
209 |
0.00 % |
0 |
0.00 % |
209 |
0.00 % |
| q20,qd2,fs60 |
93 |
0.00 % |
0 |
0.00 % |
93 |
0.00 % |
| q20,qd2,fs60,mq40 |
75 |
0.00 % |
0 |
0.00 % |
75 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3388268 |
30.51 % |
| Transition |
G>A |
All |
870575 |
7.84 % |
| Transition |
T>C |
All |
3364071 |
30.29 % |
| Transition |
C>T |
All |
872341 |
7.85 % |
| Transversion |
A>C |
All |
222870 |
2.01 % |
| Transversion |
C>A |
All |
461066 |
4.15 % |
| Transversion |
T>G |
All |
225059 |
2.03 % |
| Transversion |
G>T |
All |
448531 |
4.04 % |
| Transversion |
A>T |
All |
424784 |
3.82 % |
| Transversion |
T>A |
All |
425583 |
3.83 % |
| Transversion |
C>G |
All |
201202 |
1.81 % |
| Transversion |
G>C |
All |
201506 |
1.81 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
593152 |
17.02 % |
| Transition |
G>A |
Passed |
564057 |
16.19 % |
| Transition |
T>C |
Passed |
595041 |
17.08 % |
| Transition |
C>T |
Passed |
565917 |
16.24 % |
| Transversion |
A>C |
Passed |
151292 |
4.34 % |
| Transversion |
C>A |
Passed |
152634 |
4.38 % |
| Transversion |
T>G |
Passed |
151949 |
4.36 % |
| Transversion |
G>T |
Passed |
152328 |
4.37 % |
| Transversion |
A>T |
Passed |
131801 |
3.78 % |
| Transversion |
T>A |
Passed |
131952 |
3.79 % |
| Transversion |
C>G |
Passed |
147148 |
4.22 % |
| Transversion |
G>C |
Passed |
147472 |
4.23 % |
| |
|
|
|
|
| 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 |
3.25 |
8495255 |
2610601 |
| Passed |
1.99 |
2318167 |
1166576 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |