/EXTERNAL KNIH/variants/K006246_1_lane_gembs
BACK
SAMPLE K006246_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1105261904 |
380080287 |
34.39 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1105261904 |
100% |
1053256231 |
95.29 % |
52005673 |
4.71 % |
| |
|
|
|
|
|
|
| Passed |
390425778 |
35.32 % |
374094216 |
35.52 % |
16331562 |
4.18 % |
| Filtered |
714836126 |
64.68 % |
679162015 |
64.48 % |
35674111 |
9.14 % |
| |
|
|
|
|
|
|
| q20 |
615383213 |
86.09 % |
600953279 |
88.48 % |
14429934 |
40.45 % |
| q20,qd2 |
86101431 |
12.04 % |
65727983 |
9.68 % |
20373448 |
57.11 % |
| qd2 |
5279249 |
0.74 % |
4686429 |
0.69 % |
592820 |
1.66 % |
| q20,mq40 |
4931787 |
0.69 % |
4827804 |
0.71 % |
103983 |
0.29 % |
| q20,qd2,mq40 |
2734087 |
0.38 % |
2668726 |
0.39 % |
65361 |
0.18 % |
| mq40 |
384755 |
0.05 % |
281331 |
0.04 % |
103424 |
0.29 % |
| qd2,mq40 |
20486 |
0.00 % |
16463 |
0.00 % |
4023 |
0.01 % |
| q20,qd2,fs60 |
452 |
0.00 % |
0 |
0.00 % |
452 |
0.00 % |
| fs60 |
411 |
0.00 % |
0 |
0.00 % |
411 |
0.00 % |
| qd2,fs60 |
139 |
0.00 % |
0 |
0.00 % |
139 |
0.00 % |
| qd2,fs60,mq40 |
48 |
0.00 % |
0 |
0.00 % |
48 |
0.00 % |
| fs60,mq40 |
44 |
0.00 % |
0 |
0.00 % |
44 |
0.00 % |
| q20,qd2,fs60,mq40 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
15576272 |
28.42 % |
| Transition |
G>A |
All |
3326295 |
6.07 % |
| Transition |
T>C |
All |
15362120 |
28.03 % |
| Transition |
C>T |
All |
2366606 |
4.32 % |
| Transversion |
A>C |
All |
1327798 |
2.42 % |
| Transversion |
C>A |
All |
4532681 |
8.27 % |
| Transversion |
T>G |
All |
1517007 |
2.77 % |
| Transversion |
G>T |
All |
4312356 |
7.87 % |
| Transversion |
A>T |
All |
1979674 |
3.61 % |
| Transversion |
T>A |
All |
2256265 |
4.12 % |
| Transversion |
C>G |
All |
1121306 |
2.05 % |
| Transversion |
G>C |
All |
1128899 |
2.06 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1718576 |
27.18 % |
| Transition |
G>A |
Passed |
655479 |
10.37 % |
| Transition |
T>C |
Passed |
2282002 |
36.09 % |
| Transition |
C>T |
Passed |
425741 |
6.73 % |
| Transversion |
A>C |
Passed |
153708 |
2.43 % |
| Transversion |
C>A |
Passed |
184957 |
2.93 % |
| Transversion |
T>G |
Passed |
171679 |
2.72 % |
| Transversion |
G>T |
Passed |
132527 |
2.10 % |
| Transversion |
A>T |
Passed |
87399 |
1.38 % |
| Transversion |
T>A |
Passed |
133932 |
2.12 % |
| Transversion |
C>G |
Passed |
180797 |
2.86 % |
| Transversion |
G>C |
Passed |
195620 |
3.09 % |
| |
|
|
|
|
| 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 |
2.02 |
36631293 |
18175986 |
| Passed |
4.10 |
5081798 |
1240619 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |