/EXTERNAL KNIH/variants/K006237_1_lane_gembs
BACK
SAMPLE K006237_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1206309901 |
851721046 |
70.61 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1206309901 |
100% |
1147014325 |
95.08 % |
59295576 |
4.92 % |
| |
|
|
|
|
|
|
| Passed |
861089206 |
71.38 % |
841190480 |
73.34 % |
19898726 |
2.31 % |
| Filtered |
345220695 |
28.62 % |
305823845 |
26.66 % |
39396850 |
4.58 % |
| |
|
|
|
|
|
|
| q20 |
283122487 |
82.01 % |
271609492 |
88.81 % |
11512995 |
29.22 % |
| q20,qd2 |
40176329 |
11.64 % |
15057405 |
4.92 % |
25118924 |
63.76 % |
| qd2 |
13916115 |
4.03 % |
11690368 |
3.82 % |
2225747 |
5.65 % |
| q20,mq40 |
5095164 |
1.48 % |
4917726 |
1.61 % |
177438 |
0.45 % |
| q20,qd2,mq40 |
2082518 |
0.60 % |
1952988 |
0.64 % |
129530 |
0.33 % |
| mq40 |
786484 |
0.23 % |
573007 |
0.19 % |
213477 |
0.54 % |
| qd2,mq40 |
29815 |
0.01 % |
22859 |
0.01 % |
6956 |
0.02 % |
| fs60 |
7101 |
0.00 % |
0 |
0.00 % |
7101 |
0.02 % |
| q20,qd2,fs60 |
2972 |
0.00 % |
0 |
0.00 % |
2972 |
0.01 % |
| qd2,fs60 |
1138 |
0.00 % |
0 |
0.00 % |
1138 |
0.00 % |
| fs60,mq40 |
205 |
0.00 % |
0 |
0.00 % |
205 |
0.00 % |
| qd2,fs60,mq40 |
184 |
0.00 % |
0 |
0.00 % |
184 |
0.00 % |
| q20,fs60 |
135 |
0.00 % |
0 |
0.00 % |
135 |
0.00 % |
| q20,qd2,fs60,mq40 |
46 |
0.00 % |
0 |
0.00 % |
46 |
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 |
19844606 |
32.24 % |
| Transition |
G>A |
All |
4634081 |
7.53 % |
| Transition |
T>C |
All |
23528176 |
38.22 % |
| Transition |
C>T |
All |
3307051 |
5.37 % |
| Transversion |
A>C |
All |
1133336 |
1.84 % |
| Transversion |
C>A |
All |
1684632 |
2.74 % |
| Transversion |
T>G |
All |
1237851 |
2.01 % |
| Transversion |
G>T |
All |
1599173 |
2.60 % |
| Transversion |
A>T |
All |
1447270 |
2.35 % |
| Transversion |
T>A |
All |
1597005 |
2.59 % |
| Transversion |
C>G |
All |
779381 |
1.27 % |
| Transversion |
G>C |
All |
765147 |
1.24 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2752985 |
23.93 % |
| Transition |
G>A |
Passed |
1003646 |
8.72 % |
| Transition |
T>C |
Passed |
5124289 |
44.54 % |
| Transition |
C>T |
Passed |
743273 |
6.46 % |
| Transversion |
A>C |
Passed |
236716 |
2.06 % |
| Transversion |
C>A |
Passed |
282086 |
2.45 % |
| Transversion |
T>G |
Passed |
255773 |
2.22 % |
| Transversion |
G>T |
Passed |
224432 |
1.95 % |
| Transversion |
A>T |
Passed |
183833 |
1.60 % |
| Transversion |
T>A |
Passed |
241592 |
2.10 % |
| Transversion |
C>G |
Passed |
229328 |
1.99 % |
| Transversion |
G>C |
Passed |
227044 |
1.97 % |
| |
|
|
|
|
| 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 |
5.01 |
51313914 |
10243795 |
| Passed |
5.12 |
9624193 |
1880804 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |