/EXTERNAL BLUEPRINT/variants/K006339_11_lane_gembs
BACK
SAMPLE K006339_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1119512708 |
648523105 |
57.93 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1119512708 |
100% |
1104903336 |
98.70 % |
14609372 |
1.30 % |
| |
|
|
|
|
|
|
| Passed |
650276539 |
58.09 % |
647153322 |
58.57 % |
3123217 |
0.48 % |
| Filtered |
469236169 |
41.91 % |
457750014 |
41.43 % |
11486155 |
1.77 % |
| |
|
|
|
|
|
|
| q20 |
401303971 |
85.52 % |
399664900 |
87.31 % |
1639071 |
14.27 % |
| q20,qd2 |
41862065 |
8.92 % |
32579583 |
7.12 % |
9282482 |
80.81 % |
| q20,mq40 |
14734702 |
3.14 % |
14624064 |
3.19 % |
110638 |
0.96 % |
| mq40 |
5954020 |
1.27 % |
5790795 |
1.27 % |
163225 |
1.42 % |
| q20,qd2,mq40 |
3323844 |
0.71 % |
3130029 |
0.68 % |
193815 |
1.69 % |
| qd2 |
1977831 |
0.42 % |
1896686 |
0.41 % |
81145 |
0.71 % |
| qd2,mq40 |
74578 |
0.02 % |
63957 |
0.01 % |
10621 |
0.09 % |
| q20,qd2,fs60 |
1484 |
0.00 % |
0 |
0.00 % |
1484 |
0.01 % |
| fs60 |
1133 |
0.00 % |
0 |
0.00 % |
1133 |
0.01 % |
| qd2,fs60,mq40 |
945 |
0.00 % |
0 |
0.00 % |
945 |
0.01 % |
| qd2,fs60 |
698 |
0.00 % |
0 |
0.00 % |
698 |
0.01 % |
| q20,qd2,fs60,mq40 |
484 |
0.00 % |
0 |
0.00 % |
484 |
0.00 % |
| fs60,mq40 |
413 |
0.00 % |
0 |
0.00 % |
413 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3264806 |
19.35 % |
| Transition |
G>A |
All |
3823230 |
22.66 % |
| Transition |
T>C |
All |
3106753 |
18.41 % |
| Transition |
C>T |
All |
3698505 |
21.92 % |
| Transversion |
A>C |
All |
229639 |
1.36 % |
| Transversion |
C>A |
All |
590044 |
3.50 % |
| Transversion |
T>G |
All |
244145 |
1.45 % |
| Transversion |
G>T |
All |
586986 |
3.48 % |
| Transversion |
A>T |
All |
473666 |
2.81 % |
| Transversion |
T>A |
All |
466405 |
2.76 % |
| Transversion |
C>G |
All |
198029 |
1.17 % |
| Transversion |
G>C |
All |
190386 |
1.13 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
376888 |
18.54 % |
| Transition |
G>A |
Passed |
345758 |
17.01 % |
| Transition |
T>C |
Passed |
375978 |
18.49 % |
| Transition |
C>T |
Passed |
346222 |
17.03 % |
| Transversion |
A>C |
Passed |
78723 |
3.87 % |
| Transversion |
C>A |
Passed |
72491 |
3.57 % |
| Transversion |
T>G |
Passed |
78620 |
3.87 % |
| Transversion |
G>T |
Passed |
72766 |
3.58 % |
| Transversion |
A>T |
Passed |
50229 |
2.47 % |
| Transversion |
T>A |
Passed |
50270 |
2.47 % |
| Transversion |
C>G |
Passed |
92031 |
4.53 % |
| Transversion |
G>C |
Passed |
93234 |
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 |
4.66 |
13893294 |
2979300 |
| Passed |
2.46 |
1444846 |
588364 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |