/EXTERNAL BLUEPRINT/variants/K012133_1_lane_gembs
BACK
SAMPLE K012133_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
480560978 |
186498 |
0.04 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
480560978 |
100% |
477124895 |
99.28 % |
3436083 |
0.72 % |
| |
|
|
|
|
|
|
| Passed |
1848625 |
0.38 % |
146483 |
0.03 % |
1702142 |
92.08 % |
| Filtered |
478712353 |
99.62 % |
476978412 |
99.97 % |
1733941 |
93.80 % |
| |
|
|
|
|
|
|
| q20 |
297698164 |
62.19 % |
296302634 |
62.12 % |
1395530 |
80.48 % |
| q20,qd2 |
138791756 |
28.99 % |
138650692 |
29.07 % |
141064 |
8.14 % |
| q20,mq40 |
26017758 |
5.43 % |
25927675 |
5.44 % |
90083 |
5.20 % |
| q20,qd2,mq40 |
16095317 |
3.36 % |
16083520 |
3.37 % |
11797 |
0.68 % |
| mq40 |
107655 |
0.02 % |
12302 |
0.00 % |
95353 |
5.50 % |
| qd2 |
1416 |
0.00 % |
1374 |
0.00 % |
42 |
0.00 % |
| qd2,mq40 |
270 |
0.00 % |
215 |
0.00 % |
55 |
0.00 % |
| fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,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 |
1586944 |
23.07 % |
| Transition |
G>A |
All |
573648 |
8.34 % |
| Transition |
T>C |
All |
2125176 |
30.90 % |
| Transition |
C>T |
All |
286771 |
4.17 % |
| Transversion |
A>C |
All |
244994 |
3.56 % |
| Transversion |
C>A |
All |
334204 |
4.86 % |
| Transversion |
T>G |
All |
312444 |
4.54 % |
| Transversion |
G>T |
All |
292530 |
4.25 % |
| Transversion |
A>T |
All |
265633 |
3.86 % |
| Transversion |
T>A |
All |
379642 |
5.52 % |
| Transversion |
C>G |
All |
219534 |
3.19 % |
| Transversion |
G>C |
All |
257054 |
3.74 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
6199 |
15.87 % |
| Transition |
G>A |
Passed |
6722 |
17.21 % |
| Transition |
T>C |
Passed |
9600 |
24.58 % |
| Transition |
C>T |
Passed |
2843 |
7.28 % |
| Transversion |
A>C |
Passed |
1466 |
3.75 % |
| Transversion |
C>A |
Passed |
2091 |
5.35 % |
| Transversion |
T>G |
Passed |
1679 |
4.30 % |
| Transversion |
G>T |
Passed |
1089 |
2.79 % |
| Transversion |
A>T |
Passed |
708 |
1.81 % |
| Transversion |
T>A |
Passed |
1780 |
4.56 % |
| Transversion |
C>G |
Passed |
1951 |
5.00 % |
| Transversion |
G>C |
Passed |
2925 |
7.49 % |
| |
|
|
|
|
| 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 |
1.98 |
4572539 |
2306035 |
| Passed |
1.85 |
25364 |
13689 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |