/EXTERNAL BLUEPRINT/variants/K006259_19_lane_gembs
BACK
SAMPLE K006259_19_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1149313122 |
862555363 |
75.05 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1149313122 |
100% |
1131854056 |
98.48 % |
17459066 |
1.52 % |
| |
|
|
|
|
|
|
| Passed |
863871188 |
75.16 % |
860767378 |
76.05 % |
3103810 |
0.36 % |
| Filtered |
285441934 |
24.84 % |
271086678 |
23.95 % |
14355256 |
1.66 % |
| |
|
|
|
|
|
|
| q20 |
223575986 |
78.33 % |
222231857 |
81.98 % |
1344129 |
9.36 % |
| q20,qd2 |
29792730 |
10.44 % |
17641804 |
6.51 % |
12150926 |
84.64 % |
| q20,mq40 |
14481003 |
5.07 % |
14339935 |
5.29 % |
141068 |
0.98 % |
| mq40 |
10821881 |
3.79 % |
10562372 |
3.90 % |
259509 |
1.81 % |
| qd2 |
3472352 |
1.22 % |
3328034 |
1.23 % |
144318 |
1.01 % |
| q20,qd2,mq40 |
3116979 |
1.09 % |
2835690 |
1.05 % |
281289 |
1.96 % |
| qd2,mq40 |
164391 |
0.06 % |
146986 |
0.05 % |
17405 |
0.12 % |
| q20,qd2,fs60 |
8309 |
0.00 % |
0 |
0.00 % |
8309 |
0.06 % |
| fs60 |
2578 |
0.00 % |
0 |
0.00 % |
2578 |
0.02 % |
| qd2,fs60,mq40 |
2142 |
0.00 % |
0 |
0.00 % |
2142 |
0.01 % |
| qd2,fs60 |
2018 |
0.00 % |
0 |
0.00 % |
2018 |
0.01 % |
| fs60,mq40 |
879 |
0.00 % |
0 |
0.00 % |
879 |
0.01 % |
| q20,qd2,fs60,mq40 |
671 |
0.00 % |
0 |
0.00 % |
671 |
0.00 % |
| q20,fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
2972311 |
12.30 % |
| Transition |
G>A |
All |
7881228 |
32.61 % |
| Transition |
T>C |
All |
2889659 |
11.96 % |
| Transition |
C>T |
All |
7771943 |
32.16 % |
| Transversion |
A>C |
All |
207137 |
0.86 % |
| Transversion |
C>A |
All |
530238 |
2.19 % |
| Transversion |
T>G |
All |
215680 |
0.89 % |
| Transversion |
G>T |
All |
532905 |
2.20 % |
| Transversion |
A>T |
All |
391926 |
1.62 % |
| Transversion |
T>A |
All |
377739 |
1.56 % |
| Transversion |
C>G |
All |
203645 |
0.84 % |
| Transversion |
G>C |
All |
195640 |
0.81 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
489813 |
18.04 % |
| Transition |
G>A |
Passed |
462072 |
17.02 % |
| Transition |
T>C |
Passed |
491069 |
18.09 % |
| Transition |
C>T |
Passed |
461695 |
17.01 % |
| Transversion |
A>C |
Passed |
105318 |
3.88 % |
| Transversion |
C>A |
Passed |
102860 |
3.79 % |
| Transversion |
T>G |
Passed |
105102 |
3.87 % |
| Transversion |
G>T |
Passed |
102423 |
3.77 % |
| Transversion |
A>T |
Passed |
78862 |
2.90 % |
| Transversion |
T>A |
Passed |
78839 |
2.90 % |
| Transversion |
C>G |
Passed |
118163 |
4.35 % |
| Transversion |
G>C |
Passed |
118484 |
4.36 % |
| |
|
|
|
|
| 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 |
8.10 |
21515141 |
2654910 |
| Passed |
2.35 |
1904649 |
810051 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |