/EXTERNAL BLUEPRINT/variants/K006358_10_lane_gembs
BACK
SAMPLE K006358_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1126642563 |
696112847 |
61.79 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1126642563 |
100% |
1113986520 |
98.88 % |
12656043 |
1.12 % |
| |
|
|
|
|
|
|
| Passed |
697821320 |
61.94 % |
694604667 |
62.35 % |
3216653 |
0.46 % |
| Filtered |
428821243 |
38.06 % |
419381853 |
37.65 % |
9439390 |
1.35 % |
| |
|
|
|
|
|
|
| q20 |
371633762 |
86.66 % |
370172004 |
88.27 % |
1461758 |
15.49 % |
| q20,qd2 |
33090607 |
7.72 % |
25640080 |
6.11 % |
7450527 |
78.93 % |
| q20,mq40 |
13278623 |
3.10 % |
13182829 |
3.14 % |
95794 |
1.01 % |
| mq40 |
5842187 |
1.36 % |
5690175 |
1.36 % |
152012 |
1.61 % |
| q20,qd2,mq40 |
2953758 |
0.69 % |
2769907 |
0.66 % |
183851 |
1.95 % |
| qd2 |
1952149 |
0.46 % |
1870552 |
0.45 % |
81597 |
0.86 % |
| qd2,mq40 |
65458 |
0.02 % |
56306 |
0.01 % |
9152 |
0.10 % |
| q20,qd2,fs60 |
1381 |
0.00 % |
0 |
0.00 % |
1381 |
0.01 % |
| fs60 |
989 |
0.00 % |
0 |
0.00 % |
989 |
0.01 % |
| qd2,fs60,mq40 |
940 |
0.00 % |
0 |
0.00 % |
940 |
0.01 % |
| qd2,fs60 |
558 |
0.00 % |
0 |
0.00 % |
558 |
0.01 % |
| fs60,mq40 |
417 |
0.00 % |
0 |
0.00 % |
417 |
0.00 % |
| q20,qd2,fs60,mq40 |
413 |
0.00 % |
0 |
0.00 % |
413 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3239053 |
22.36 % |
| Transition |
G>A |
All |
2630174 |
18.16 % |
| Transition |
T>C |
All |
3113253 |
21.49 % |
| Transition |
C>T |
All |
2533098 |
17.49 % |
| Transversion |
A>C |
All |
223173 |
1.54 % |
| Transversion |
C>A |
All |
588694 |
4.06 % |
| Transversion |
T>G |
All |
233961 |
1.62 % |
| Transversion |
G>T |
All |
578738 |
4.00 % |
| Transversion |
A>T |
All |
480296 |
3.32 % |
| Transversion |
T>A |
All |
477575 |
3.30 % |
| Transversion |
C>G |
All |
196484 |
1.36 % |
| Transversion |
G>C |
All |
190036 |
1.31 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
409402 |
18.43 % |
| Transition |
G>A |
Passed |
373466 |
16.81 % |
| Transition |
T>C |
Passed |
409915 |
18.45 % |
| Transition |
C>T |
Passed |
373335 |
16.80 % |
| Transversion |
A>C |
Passed |
88518 |
3.98 % |
| Transversion |
C>A |
Passed |
80103 |
3.61 % |
| Transversion |
T>G |
Passed |
88854 |
4.00 % |
| Transversion |
G>T |
Passed |
79933 |
3.60 % |
| Transversion |
A>T |
Passed |
57537 |
2.59 % |
| Transversion |
T>A |
Passed |
57537 |
2.59 % |
| Transversion |
C>G |
Passed |
101313 |
4.56 % |
| Transversion |
G>C |
Passed |
101957 |
4.59 % |
| |
|
|
|
|
| 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 |
3.88 |
11515578 |
2968957 |
| Passed |
2.39 |
1566118 |
655752 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |