/EXTERNAL BLUEPRINT/variants/K006263_19_lane_gembs
BACK
SAMPLE K006263_19_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1148448632 |
920031130 |
80.11 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1148448632 |
100% |
1134214485 |
98.76 % |
14234147 |
1.24 % |
| |
|
|
|
|
|
|
| Passed |
921234073 |
80.22 % |
918042496 |
80.94 % |
3191577 |
0.35 % |
| Filtered |
227214559 |
19.78 % |
216171989 |
19.06 % |
11042570 |
1.20 % |
| |
|
|
|
|
|
|
| q20 |
176136767 |
77.52 % |
174959001 |
80.94 % |
1177766 |
10.67 % |
| q20,qd2 |
20102350 |
8.85 % |
11023518 |
5.10 % |
9078832 |
82.22 % |
| q20,mq40 |
14241785 |
6.27 % |
14115643 |
6.53 % |
126142 |
1.14 % |
| mq40 |
10314249 |
4.54 % |
10070744 |
4.66 % |
243505 |
2.21 % |
| qd2 |
3241298 |
1.43 % |
3102535 |
1.44 % |
138763 |
1.26 % |
| q20,qd2,mq40 |
3026751 |
1.33 % |
2778689 |
1.29 % |
248062 |
2.25 % |
| qd2,mq40 |
139355 |
0.06 % |
121859 |
0.06 % |
17496 |
0.16 % |
| q20,qd2,fs60 |
5437 |
0.00 % |
0 |
0.00 % |
5437 |
0.05 % |
| fs60 |
2038 |
0.00 % |
0 |
0.00 % |
2038 |
0.02 % |
| qd2,fs60,mq40 |
1895 |
0.00 % |
0 |
0.00 % |
1895 |
0.02 % |
| qd2,fs60 |
1241 |
0.00 % |
0 |
0.00 % |
1241 |
0.01 % |
| fs60,mq40 |
840 |
0.00 % |
0 |
0.00 % |
840 |
0.01 % |
| q20,qd2,fs60,mq40 |
536 |
0.00 % |
0 |
0.00 % |
536 |
0.00 % |
| q20,fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
2876466 |
16.29 % |
| Transition |
G>A |
All |
4757508 |
26.94 % |
| Transition |
T>C |
All |
2755813 |
15.60 % |
| Transition |
C>T |
All |
4650130 |
26.33 % |
| Transversion |
A>C |
All |
208618 |
1.18 % |
| Transversion |
C>A |
All |
516198 |
2.92 % |
| Transversion |
T>G |
All |
217558 |
1.23 % |
| Transversion |
G>T |
All |
516281 |
2.92 % |
| Transversion |
A>T |
All |
387586 |
2.19 % |
| Transversion |
T>A |
All |
376226 |
2.13 % |
| Transversion |
C>G |
All |
201534 |
1.14 % |
| Transversion |
G>C |
All |
197173 |
1.12 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
522988 |
17.59 % |
| Transition |
G>A |
Passed |
504806 |
16.98 % |
| Transition |
T>C |
Passed |
524293 |
17.63 % |
| Transition |
C>T |
Passed |
506677 |
17.04 % |
| Transversion |
A>C |
Passed |
117898 |
3.97 % |
| Transversion |
C>A |
Passed |
118018 |
3.97 % |
| Transversion |
T>G |
Passed |
117831 |
3.96 % |
| Transversion |
G>T |
Passed |
117334 |
3.95 % |
| Transversion |
A>T |
Passed |
93029 |
3.13 % |
| Transversion |
T>A |
Passed |
92896 |
3.12 % |
| Transversion |
C>G |
Passed |
128416 |
4.32 % |
| Transversion |
G>C |
Passed |
128889 |
4.34 % |
| |
|
|
|
|
| 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 |
5.74 |
15039917 |
2621174 |
| Passed |
2.25 |
2058764 |
914311 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |