/EXTERNAL BLUEPRINT/variants/K011719_1_lane_gembs
BACK
SAMPLE K011719_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
714118658 |
1162581 |
0.16 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
714118658 |
100% |
705091381 |
98.74 % |
9027277 |
1.26 % |
| |
|
|
|
|
|
|
| Passed |
5738771 |
0.80 % |
1011205 |
0.14 % |
4727566 |
82.38 % |
| Filtered |
708379887 |
99.20 % |
704080176 |
99.86 % |
4299711 |
74.92 % |
| |
|
|
|
|
|
|
| q20 |
494900584 |
69.86 % |
491560695 |
69.82 % |
3339889 |
77.68 % |
| q20,qd2 |
154490068 |
21.81 % |
154020420 |
21.88 % |
469648 |
10.92 % |
| q20,mq40 |
39034371 |
5.51 % |
38827194 |
5.51 % |
207177 |
4.82 % |
| q20,qd2,mq40 |
19663696 |
2.78 % |
19631587 |
2.79 % |
32109 |
0.75 % |
| mq40 |
285450 |
0.04 % |
34797 |
0.00 % |
250653 |
5.83 % |
| qd2 |
5008 |
0.00 % |
4930 |
0.00 % |
78 |
0.00 % |
| qd2,mq40 |
672 |
0.00 % |
553 |
0.00 % |
119 |
0.00 % |
| qd2,fs60 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3117798 |
23.34 % |
| Transition |
G>A |
All |
1050610 |
7.87 % |
| Transition |
T>C |
All |
4043579 |
30.27 % |
| Transition |
C>T |
All |
522138 |
3.91 % |
| Transversion |
A>C |
All |
497818 |
3.73 % |
| Transversion |
C>A |
All |
701127 |
5.25 % |
| Transversion |
T>G |
All |
601975 |
4.51 % |
| Transversion |
G>T |
All |
635844 |
4.76 % |
| Transversion |
A>T |
All |
524586 |
3.93 % |
| Transversion |
T>A |
All |
721346 |
5.40 % |
| Transversion |
C>G |
All |
432294 |
3.24 % |
| Transversion |
G>C |
All |
507781 |
3.80 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
23622 |
15.85 % |
| Transition |
G>A |
Passed |
22460 |
15.07 % |
| Transition |
T>C |
Passed |
40661 |
27.29 % |
| Transition |
C>T |
Passed |
10040 |
6.74 % |
| Transversion |
A>C |
Passed |
6100 |
4.09 % |
| Transversion |
C>A |
Passed |
8156 |
5.47 % |
| Transversion |
T>G |
Passed |
6277 |
4.21 % |
| Transversion |
G>T |
Passed |
4927 |
3.31 % |
| Transversion |
A>T |
Passed |
2906 |
1.95 % |
| Transversion |
T>A |
Passed |
7006 |
4.70 % |
| Transversion |
C>G |
Passed |
6813 |
4.57 % |
| Transversion |
G>C |
Passed |
10027 |
6.73 % |
| |
|
|
|
|
| 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 |
1.89 |
8734125 |
4622771 |
| Passed |
1.85 |
96783 |
52212 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |