/EXTERNAL BLUEPRINT/variants/K006307_K006317_21_lane_gembs
BACK
SAMPLE K006307_K006317_21_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1033620552 |
465070917 |
44.99 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1033620552 |
100% |
1017285899 |
98.42 % |
16334653 |
1.58 % |
| |
|
|
|
|
|
|
| Passed |
466711375 |
45.15 % |
464174219 |
45.63 % |
2537156 |
0.54 % |
| Filtered |
566909177 |
54.85 % |
553111680 |
54.37 % |
13797497 |
2.96 % |
| |
|
|
|
|
|
|
| q20 |
458603575 |
80.90 % |
456818202 |
82.59 % |
1785373 |
12.94 % |
| q20,qd2 |
70088891 |
12.36 % |
58567012 |
10.59 % |
11521879 |
83.51 % |
| q20,mq40 |
15457485 |
2.73 % |
15375156 |
2.78 % |
82329 |
0.60 % |
| qd2 |
12602518 |
2.22 % |
12507950 |
2.26 % |
94568 |
0.69 % |
| mq40 |
6446055 |
1.14 % |
6302552 |
1.14 % |
143503 |
1.04 % |
| q20,qd2,mq40 |
3597351 |
0.63 % |
3455002 |
0.62 % |
142349 |
1.03 % |
| qd2,mq40 |
99170 |
0.02 % |
85806 |
0.02 % |
13364 |
0.10 % |
| q20,qd2,fs60 |
4294 |
0.00 % |
0 |
0.00 % |
4294 |
0.03 % |
| qd2,fs60 |
4020 |
0.00 % |
0 |
0.00 % |
4020 |
0.03 % |
| fs60 |
2199 |
0.00 % |
0 |
0.00 % |
2199 |
0.02 % |
| qd2,fs60,mq40 |
2049 |
0.00 % |
0 |
0.00 % |
2049 |
0.01 % |
| q20,qd2,fs60,mq40 |
921 |
0.00 % |
0 |
0.00 % |
921 |
0.01 % |
| fs60,mq40 |
647 |
0.00 % |
0 |
0.00 % |
647 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,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 |
2920403 |
10.10 % |
| Transition |
G>A |
All |
10586285 |
36.59 % |
| Transition |
T>C |
All |
2633794 |
9.10 % |
| Transition |
C>T |
All |
10462266 |
36.17 % |
| Transversion |
A>C |
All |
188046 |
0.65 % |
| Transversion |
C>A |
All |
459140 |
1.59 % |
| Transversion |
T>G |
All |
215330 |
0.74 % |
| Transversion |
G>T |
All |
441120 |
1.52 % |
| Transversion |
A>T |
All |
327145 |
1.13 % |
| Transversion |
T>A |
All |
341939 |
1.18 % |
| Transversion |
C>G |
All |
184382 |
0.64 % |
| Transversion |
G>C |
All |
168789 |
0.58 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
276166 |
20.27 % |
| Transition |
G>A |
Passed |
231924 |
17.02 % |
| Transition |
T>C |
Passed |
273368 |
20.06 % |
| Transition |
C>T |
Passed |
230771 |
16.93 % |
| Transversion |
A>C |
Passed |
46964 |
3.45 % |
| Transversion |
C>A |
Passed |
41138 |
3.02 % |
| Transversion |
T>G |
Passed |
46649 |
3.42 % |
| Transversion |
G>T |
Passed |
40809 |
2.99 % |
| Transversion |
A>T |
Passed |
25082 |
1.84 % |
| Transversion |
T>A |
Passed |
24746 |
1.82 % |
| Transversion |
C>G |
Passed |
62318 |
4.57 % |
| Transversion |
G>C |
Passed |
62822 |
4.61 % |
| |
|
|
|
|
| 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 |
11.44 |
26602748 |
2325891 |
| Passed |
2.89 |
1012229 |
350528 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |