/EXTERNAL KNIH/variants/K006254_1_lane_gembs
BACK
SAMPLE K006254_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1199929327 |
696209643 |
58.02 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1199929327 |
100% |
1130394697 |
94.21 % |
69534630 |
5.79 % |
| |
|
|
|
|
|
|
| Passed |
708415078 |
59.04 % |
686331395 |
60.72 % |
22083683 |
3.12 % |
| Filtered |
491514249 |
40.96 % |
444063302 |
39.28 % |
47450947 |
6.70 % |
| |
|
|
|
|
|
|
| q20 |
421727691 |
85.80 % |
403937384 |
90.96 % |
17790307 |
37.49 % |
| q20,qd2 |
52340294 |
10.65 % |
24620120 |
5.54 % |
27720174 |
58.42 % |
| qd2 |
9213096 |
1.87 % |
7735143 |
1.74 % |
1477953 |
3.11 % |
| q20,mq40 |
5288424 |
1.08 % |
5112618 |
1.15 % |
175806 |
0.37 % |
| q20,qd2,mq40 |
2340589 |
0.48 % |
2237191 |
0.50 % |
103398 |
0.22 % |
| mq40 |
581419 |
0.12 % |
405208 |
0.09 % |
176211 |
0.37 % |
| qd2,mq40 |
20677 |
0.00 % |
15638 |
0.00 % |
5039 |
0.01 % |
| fs60 |
1088 |
0.00 % |
0 |
0.00 % |
1088 |
0.00 % |
| q20,qd2,fs60 |
525 |
0.00 % |
0 |
0.00 % |
525 |
0.00 % |
| qd2,fs60 |
259 |
0.00 % |
0 |
0.00 % |
259 |
0.00 % |
| fs60,mq40 |
86 |
0.00 % |
0 |
0.00 % |
86 |
0.00 % |
| qd2,fs60,mq40 |
70 |
0.00 % |
0 |
0.00 % |
70 |
0.00 % |
| q20,qd2,fs60,mq40 |
21 |
0.00 % |
0 |
0.00 % |
21 |
0.00 % |
| q20,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
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 |
24160614 |
33.59 % |
| Transition |
G>A |
All |
5068385 |
7.05 % |
| Transition |
T>C |
All |
26496003 |
36.83 % |
| Transition |
C>T |
All |
3261822 |
4.53 % |
| Transversion |
A>C |
All |
1572436 |
2.19 % |
| Transversion |
C>A |
All |
2061350 |
2.87 % |
| Transversion |
T>G |
All |
1702946 |
2.37 % |
| Transversion |
G>T |
All |
1922497 |
2.67 % |
| Transversion |
A>T |
All |
1628620 |
2.26 % |
| Transversion |
T>A |
All |
1858968 |
2.58 % |
| Transversion |
C>G |
All |
1079892 |
1.50 % |
| Transversion |
G>C |
All |
1121050 |
1.56 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2628697 |
24.81 % |
| Transition |
G>A |
Passed |
992988 |
9.37 % |
| Transition |
T>C |
Passed |
4491033 |
42.39 % |
| Transition |
C>T |
Passed |
644616 |
6.08 % |
| Transversion |
A>C |
Passed |
227457 |
2.15 % |
| Transversion |
C>A |
Passed |
293072 |
2.77 % |
| Transversion |
T>G |
Passed |
242722 |
2.29 % |
| Transversion |
G>T |
Passed |
220871 |
2.08 % |
| Transversion |
A>T |
Passed |
161228 |
1.52 % |
| Transversion |
T>A |
Passed |
233666 |
2.21 % |
| Transversion |
C>G |
Passed |
223779 |
2.11 % |
| Transversion |
G>C |
Passed |
235181 |
2.22 % |
| |
|
|
|
|
| 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 |
4.56 |
58986824 |
12947759 |
| Passed |
4.76 |
8757334 |
1837976 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |