/EXTERNAL BLUEPRINT/variants/K006294_9_lane_gembs
BACK
SAMPLE K006294_9_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1114994586 |
664069863 |
59.56 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1114994586 |
100% |
1095402810 |
98.24 % |
19591776 |
1.76 % |
| |
|
|
|
|
|
|
| Passed |
665974622 |
59.73 % |
662679995 |
60.50 % |
3294627 |
0.49 % |
| Filtered |
449019964 |
40.27 % |
432722815 |
39.50 % |
16297149 |
2.45 % |
| |
|
|
|
|
|
|
| q20 |
373348668 |
83.15 % |
370717202 |
85.67 % |
2631466 |
16.15 % |
| q20,qd2 |
47406011 |
10.56 % |
34359815 |
7.94 % |
13046196 |
80.05 % |
| q20,mq40 |
15088206 |
3.36 % |
14963535 |
3.46 % |
124671 |
0.76 % |
| mq40 |
6925535 |
1.54 % |
6738159 |
1.56 % |
187376 |
1.15 % |
| q20,qd2,mq40 |
3424025 |
0.76 % |
3226998 |
0.75 % |
197027 |
1.21 % |
| qd2 |
2732208 |
0.61 % |
2640829 |
0.61 % |
91379 |
0.56 % |
| qd2,mq40 |
88295 |
0.02 % |
76277 |
0.02 % |
12018 |
0.07 % |
| q20,qd2,fs60 |
2356 |
0.00 % |
0 |
0.00 % |
2356 |
0.01 % |
| fs60 |
1401 |
0.00 % |
0 |
0.00 % |
1401 |
0.01 % |
| qd2,fs60,mq40 |
1203 |
0.00 % |
0 |
0.00 % |
1203 |
0.01 % |
| qd2,fs60 |
870 |
0.00 % |
0 |
0.00 % |
870 |
0.01 % |
| q20,qd2,fs60,mq40 |
608 |
0.00 % |
0 |
0.00 % |
608 |
0.00 % |
| fs60,mq40 |
574 |
0.00 % |
0 |
0.00 % |
574 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
3701863 |
15.12 % |
| Transition |
G>A |
All |
7054631 |
28.81 % |
| Transition |
T>C |
All |
3648562 |
14.90 % |
| Transition |
C>T |
All |
6918792 |
28.25 % |
| Transversion |
A>C |
All |
225872 |
0.92 % |
| Transversion |
C>A |
All |
605476 |
2.47 % |
| Transversion |
T>G |
All |
227272 |
0.93 % |
| Transversion |
G>T |
All |
604395 |
2.47 % |
| Transversion |
A>T |
All |
546940 |
2.23 % |
| Transversion |
T>A |
All |
536223 |
2.19 % |
| Transversion |
C>G |
All |
212597 |
0.87 % |
| Transversion |
G>C |
All |
208109 |
0.85 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
386731 |
18.68 % |
| Transition |
G>A |
Passed |
358491 |
17.31 % |
| Transition |
T>C |
Passed |
387612 |
18.72 % |
| Transition |
C>T |
Passed |
358604 |
17.32 % |
| Transversion |
A>C |
Passed |
75722 |
3.66 % |
| Transversion |
C>A |
Passed |
71630 |
3.46 % |
| Transversion |
T>G |
Passed |
75499 |
3.65 % |
| Transversion |
G>T |
Passed |
71573 |
3.46 % |
| Transversion |
A>T |
Passed |
50477 |
2.44 % |
| Transversion |
T>A |
Passed |
50065 |
2.42 % |
| Transversion |
C>G |
Passed |
91878 |
4.44 % |
| Transversion |
G>C |
Passed |
92563 |
4.47 % |
| |
|
|
|
|
| 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 |
6.73 |
21323848 |
3166884 |
| Passed |
2.57 |
1491438 |
579407 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |