/EXTERNAL KNIH/variants/K006234_1_lane_gembs
BACK
SAMPLE K006234_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1200749665 |
837580423 |
69.75 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1200749665 |
100% |
1140318785 |
94.97 % |
60430880 |
5.03 % |
| |
|
|
|
|
|
|
| Passed |
847449002 |
70.58 % |
826723624 |
72.50 % |
20725378 |
2.45 % |
| Filtered |
353300663 |
29.42 % |
313595161 |
27.50 % |
39705502 |
4.69 % |
| |
|
|
|
|
|
|
| q20 |
292065178 |
82.67 % |
280851944 |
89.56 % |
11213234 |
28.24 % |
| q20,qd2 |
40759719 |
11.54 % |
14973854 |
4.77 % |
25785865 |
64.94 % |
| qd2 |
12722921 |
3.60 % |
10498999 |
3.35 % |
2223922 |
5.60 % |
| q20,mq40 |
4927827 |
1.39 % |
4772302 |
1.52 % |
155525 |
0.39 % |
| q20,qd2,mq40 |
2036885 |
0.58 % |
1922508 |
0.61 % |
114377 |
0.29 % |
| mq40 |
750249 |
0.21 % |
554195 |
0.18 % |
196054 |
0.49 % |
| qd2,mq40 |
28090 |
0.01 % |
21359 |
0.01 % |
6731 |
0.02 % |
| fs60 |
5016 |
0.00 % |
0 |
0.00 % |
5016 |
0.01 % |
| q20,qd2,fs60 |
3408 |
0.00 % |
0 |
0.00 % |
3408 |
0.01 % |
| qd2,fs60 |
801 |
0.00 % |
0 |
0.00 % |
801 |
0.00 % |
| fs60,mq40 |
209 |
0.00 % |
0 |
0.00 % |
209 |
0.00 % |
| qd2,fs60,mq40 |
162 |
0.00 % |
0 |
0.00 % |
162 |
0.00 % |
| q20,fs60 |
152 |
0.00 % |
0 |
0.00 % |
152 |
0.00 % |
| q20,qd2,fs60,mq40 |
44 |
0.00 % |
0 |
0.00 % |
44 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
20378494 |
32.52 % |
| Transition |
G>A |
All |
4770822 |
7.61 % |
| Transition |
T>C |
All |
23826565 |
38.02 % |
| Transition |
C>T |
All |
3390974 |
5.41 % |
| Transversion |
A>C |
All |
1080732 |
1.72 % |
| Transversion |
C>A |
All |
1738028 |
2.77 % |
| Transversion |
T>G |
All |
1195529 |
1.91 % |
| Transversion |
G>T |
All |
1641259 |
2.62 % |
| Transversion |
A>T |
All |
1468451 |
2.34 % |
| Transversion |
T>A |
All |
1623291 |
2.59 % |
| Transversion |
C>G |
All |
785010 |
1.25 % |
| Transversion |
G>C |
All |
767356 |
1.22 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2853899 |
24.21 % |
| Transition |
G>A |
Passed |
1042037 |
8.84 % |
| Transition |
T>C |
Passed |
5153613 |
43.72 % |
| Transition |
C>T |
Passed |
773928 |
6.57 % |
| Transversion |
A>C |
Passed |
240313 |
2.04 % |
| Transversion |
C>A |
Passed |
301290 |
2.56 % |
| Transversion |
T>G |
Passed |
263186 |
2.23 % |
| Transversion |
G>T |
Passed |
247728 |
2.10 % |
| Transversion |
A>T |
Passed |
193161 |
1.64 % |
| Transversion |
T>A |
Passed |
249302 |
2.11 % |
| Transversion |
C>G |
Passed |
236681 |
2.01 % |
| Transversion |
G>C |
Passed |
232882 |
1.98 % |
| |
|
|
|
|
| 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 |
5.08 |
52366855 |
10299656 |
| Passed |
5.00 |
9823477 |
1964543 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |