/EXTERNAL KNIH/variants/K006240_1_lane_gembs
BACK
SAMPLE K006240_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1203407257 |
770706010 |
64.04 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1203407257 |
100% |
1140660030 |
94.79 % |
62747227 |
5.21 % |
| |
|
|
|
|
|
|
| Passed |
782422947 |
65.02 % |
760703994 |
66.69 % |
21718953 |
2.78 % |
| Filtered |
420984310 |
34.98 % |
379956036 |
33.31 % |
41028274 |
5.24 % |
| |
|
|
|
|
|
|
| q20 |
358418902 |
85.14 % |
345831817 |
91.02 % |
12587085 |
30.68 % |
| q20,qd2 |
44890776 |
10.66 % |
18649022 |
4.91 % |
26241754 |
63.96 % |
| qd2 |
10382742 |
2.47 % |
8574475 |
2.26 % |
1808267 |
4.41 % |
| q20,mq40 |
4712344 |
1.12 % |
4581355 |
1.21 % |
130989 |
0.32 % |
| q20,qd2,mq40 |
1950148 |
0.46 % |
1861250 |
0.49 % |
88898 |
0.22 % |
| mq40 |
604844 |
0.14 % |
443427 |
0.12 % |
161417 |
0.39 % |
| qd2,mq40 |
19012 |
0.00 % |
14690 |
0.00 % |
4322 |
0.01 % |
| fs60 |
3431 |
0.00 % |
0 |
0.00 % |
3431 |
0.01 % |
| q20,qd2,fs60 |
1413 |
0.00 % |
0 |
0.00 % |
1413 |
0.00 % |
| qd2,fs60 |
404 |
0.00 % |
0 |
0.00 % |
404 |
0.00 % |
| fs60,mq40 |
133 |
0.00 % |
0 |
0.00 % |
133 |
0.00 % |
| qd2,fs60,mq40 |
85 |
0.00 % |
0 |
0.00 % |
85 |
0.00 % |
| q20,fs60 |
37 |
0.00 % |
0 |
0.00 % |
37 |
0.00 % |
| q20,qd2,fs60,mq40 |
37 |
0.00 % |
0 |
0.00 % |
37 |
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 |
21632520 |
33.34 % |
| Transition |
G>A |
All |
4566472 |
7.04 % |
| Transition |
T>C |
All |
24361413 |
37.54 % |
| Transition |
C>T |
All |
3349201 |
5.16 % |
| Transversion |
A>C |
All |
1139723 |
1.76 % |
| Transversion |
C>A |
All |
1987087 |
3.06 % |
| Transversion |
T>G |
All |
1222984 |
1.88 % |
| Transversion |
G>T |
All |
1893279 |
2.92 % |
| Transversion |
A>T |
All |
1466691 |
2.26 % |
| Transversion |
T>A |
All |
1614683 |
2.49 % |
| Transversion |
C>G |
All |
831949 |
1.28 % |
| Transversion |
G>C |
All |
824436 |
1.27 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2646576 |
24.56 % |
| Transition |
G>A |
Passed |
941519 |
8.74 % |
| Transition |
T>C |
Passed |
4649137 |
43.15 % |
| Transition |
C>T |
Passed |
719163 |
6.67 % |
| Transversion |
A>C |
Passed |
223871 |
2.08 % |
| Transversion |
C>A |
Passed |
280584 |
2.60 % |
| Transversion |
T>G |
Passed |
234828 |
2.18 % |
| Transversion |
G>T |
Passed |
236244 |
2.19 % |
| Transversion |
A>T |
Passed |
174226 |
1.62 % |
| Transversion |
T>A |
Passed |
221741 |
2.06 % |
| Transversion |
C>G |
Passed |
223544 |
2.07 % |
| Transversion |
G>C |
Passed |
224084 |
2.08 % |
| |
|
|
|
|
| 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 |
4.91 |
53909606 |
10980832 |
| Passed |
4.92 |
8956395 |
1819122 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |