/EXTERNAL BLUEPRINT/variants/K006297_K006298_14_lane_gembs
BACK
SAMPLE K006297_K006298_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1096253993 |
602684281 |
54.98 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1096253993 |
100% |
1078158865 |
98.35 % |
18095128 |
1.65 % |
| |
|
|
|
|
|
|
| Passed |
604144265 |
55.11 % |
601473534 |
55.79 % |
2670731 |
0.44 % |
| Filtered |
492109728 |
44.89 % |
476685331 |
44.21 % |
15424397 |
2.55 % |
| |
|
|
|
|
|
|
| q20 |
408710900 |
83.05 % |
406883907 |
85.36 % |
1826993 |
11.84 % |
| q20,qd2 |
55302450 |
11.24 % |
42240600 |
8.86 % |
13061850 |
84.68 % |
| q20,mq40 |
14953591 |
3.04 % |
14849989 |
3.12 % |
103602 |
0.67 % |
| mq40 |
6425747 |
1.31 % |
6267264 |
1.31 % |
158483 |
1.03 % |
| q20,qd2,mq40 |
3444034 |
0.70 % |
3268693 |
0.69 % |
175341 |
1.14 % |
| qd2 |
3178938 |
0.65 % |
3100546 |
0.65 % |
78392 |
0.51 % |
| qd2,mq40 |
85615 |
0.02 % |
74332 |
0.02 % |
11283 |
0.07 % |
| q20,qd2,fs60 |
2510 |
0.00 % |
0 |
0.00 % |
2510 |
0.02 % |
| fs60 |
1816 |
0.00 % |
0 |
0.00 % |
1816 |
0.01 % |
| qd2,fs60 |
1577 |
0.00 % |
0 |
0.00 % |
1577 |
0.01 % |
| qd2,fs60,mq40 |
1371 |
0.00 % |
0 |
0.00 % |
1371 |
0.01 % |
| q20,qd2,fs60,mq40 |
621 |
0.00 % |
0 |
0.00 % |
621 |
0.00 % |
| fs60,mq40 |
554 |
0.00 % |
0 |
0.00 % |
554 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
2756348 |
10.98 % |
| Transition |
G>A |
All |
8380920 |
33.39 % |
| Transition |
T>C |
All |
2610255 |
10.40 % |
| Transition |
C>T |
All |
8271077 |
32.95 % |
| Transversion |
A>C |
All |
231074 |
0.92 % |
| Transversion |
C>A |
All |
661225 |
2.63 % |
| Transversion |
T>G |
All |
251820 |
1.00 % |
| Transversion |
G>T |
All |
647731 |
2.58 % |
| Transversion |
A>T |
All |
441708 |
1.76 % |
| Transversion |
T>A |
All |
435644 |
1.74 % |
| Transversion |
C>G |
All |
212840 |
0.85 % |
| Transversion |
G>C |
All |
199141 |
0.79 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
342585 |
18.80 % |
| Transition |
G>A |
Passed |
317214 |
17.40 % |
| Transition |
T>C |
Passed |
341972 |
18.76 % |
| Transition |
C>T |
Passed |
316529 |
17.37 % |
| Transversion |
A>C |
Passed |
66683 |
3.66 % |
| Transversion |
C>A |
Passed |
61301 |
3.36 % |
| Transversion |
T>G |
Passed |
66317 |
3.64 % |
| Transversion |
G>T |
Passed |
61071 |
3.35 % |
| Transversion |
A>T |
Passed |
41875 |
2.30 % |
| Transversion |
T>A |
Passed |
41319 |
2.27 % |
| Transversion |
C>G |
Passed |
82703 |
4.54 % |
| Transversion |
G>C |
Passed |
83164 |
4.56 % |
| |
|
|
|
|
| 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 |
7.15 |
22018600 |
3081183 |
| Passed |
2.61 |
1318300 |
504433 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |