/EXTERNAL KNIH/variants/K006238_1_lane_gembs
BACK
SAMPLE K006238_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1207362124 |
821697534 |
68.06 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1207362124 |
100% |
1145330329 |
94.86 % |
62031795 |
5.14 % |
| |
|
|
|
|
|
|
| Passed |
831708490 |
68.89 % |
811049369 |
70.81 % |
20659121 |
2.48 % |
| Filtered |
375653634 |
31.11 % |
334280960 |
29.19 % |
41372674 |
4.97 % |
| |
|
|
|
|
|
|
| q20 |
310808376 |
82.74 % |
298186665 |
89.20 % |
12621711 |
30.51 % |
| q20,qd2 |
42951968 |
11.43 % |
16922710 |
5.06 % |
26029258 |
62.91 % |
| qd2 |
13750834 |
3.66 % |
11573244 |
3.46 % |
2177590 |
5.26 % |
| q20,mq40 |
5198597 |
1.38 % |
5014560 |
1.50 % |
184037 |
0.44 % |
| q20,qd2,mq40 |
2165324 |
0.58 % |
2035799 |
0.61 % |
129525 |
0.31 % |
| mq40 |
740710 |
0.20 % |
526225 |
0.16 % |
214485 |
0.52 % |
| qd2,mq40 |
28265 |
0.01 % |
21757 |
0.01 % |
6508 |
0.02 % |
| fs60 |
5439 |
0.00 % |
0 |
0.00 % |
5439 |
0.01 % |
| q20,qd2,fs60 |
2691 |
0.00 % |
0 |
0.00 % |
2691 |
0.01 % |
| qd2,fs60 |
924 |
0.00 % |
0 |
0.00 % |
924 |
0.00 % |
| fs60,mq40 |
207 |
0.00 % |
0 |
0.00 % |
207 |
0.00 % |
| qd2,fs60,mq40 |
150 |
0.00 % |
0 |
0.00 % |
150 |
0.00 % |
| q20,fs60 |
101 |
0.00 % |
0 |
0.00 % |
101 |
0.00 % |
| q20,qd2,fs60,mq40 |
47 |
0.00 % |
0 |
0.00 % |
47 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
20588598 |
32.00 % |
| Transition |
G>A |
All |
4719351 |
7.33 % |
| Transition |
T>C |
All |
24102913 |
37.46 % |
| Transition |
C>T |
All |
3359783 |
5.22 % |
| Transversion |
A>C |
All |
1347121 |
2.09 % |
| Transversion |
C>A |
All |
1912685 |
2.97 % |
| Transversion |
T>G |
All |
1465161 |
2.28 % |
| Transversion |
G>T |
All |
1822238 |
2.83 % |
| Transversion |
A>T |
All |
1544151 |
2.40 % |
| Transversion |
T>A |
All |
1705971 |
2.65 % |
| Transversion |
C>G |
All |
894785 |
1.39 % |
| Transversion |
G>C |
All |
879540 |
1.37 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2816068 |
24.34 % |
| Transition |
G>A |
Passed |
1012675 |
8.75 % |
| Transition |
T>C |
Passed |
5067477 |
43.81 % |
| Transition |
C>T |
Passed |
738448 |
6.38 % |
| Transversion |
A>C |
Passed |
241799 |
2.09 % |
| Transversion |
C>A |
Passed |
295254 |
2.55 % |
| Transversion |
T>G |
Passed |
262081 |
2.27 % |
| Transversion |
G>T |
Passed |
234701 |
2.03 % |
| Transversion |
A>T |
Passed |
183786 |
1.59 % |
| Transversion |
T>A |
Passed |
244894 |
2.12 % |
| Transversion |
C>G |
Passed |
236484 |
2.04 % |
| Transversion |
G>C |
Passed |
234250 |
2.02 % |
| |
|
|
|
|
| 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 |
52770645 |
11571652 |
| Passed |
4.98 |
9634668 |
1933249 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |