/EXTERNAL BLUEPRINT/variants/K006353_12_lane_gembs
BACK
SAMPLE K006353_12_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1089159063 |
581417324 |
53.38 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1089159063 |
100% |
1073681283 |
98.58 % |
15477780 |
1.42 % |
| |
|
|
|
|
|
|
| Passed |
582947573 |
53.52 % |
580224624 |
54.04 % |
2722949 |
0.47 % |
| Filtered |
506211490 |
46.48 % |
493456659 |
45.96 % |
12754831 |
2.19 % |
| |
|
|
|
|
|
|
| q20 |
426344357 |
84.22 % |
424875797 |
86.10 % |
1468560 |
11.51 % |
| q20,qd2 |
53373647 |
10.54 % |
42614046 |
8.64 % |
10759601 |
84.36 % |
| q20,mq40 |
14947685 |
2.95 % |
14845254 |
3.01 % |
102431 |
0.80 % |
| mq40 |
5951733 |
1.18 % |
5804118 |
1.18 % |
147615 |
1.16 % |
| q20,qd2,mq40 |
3435041 |
0.68 % |
3246068 |
0.66 % |
188973 |
1.48 % |
| qd2 |
2079419 |
0.41 % |
2007561 |
0.41 % |
71858 |
0.56 % |
| qd2,mq40 |
73365 |
0.01 % |
63815 |
0.01 % |
9550 |
0.07 % |
| q20,qd2,fs60 |
2145 |
0.00 % |
0 |
0.00 % |
2145 |
0.02 % |
| fs60 |
1296 |
0.00 % |
0 |
0.00 % |
1296 |
0.01 % |
| qd2,fs60,mq40 |
986 |
0.00 % |
0 |
0.00 % |
986 |
0.01 % |
| qd2,fs60 |
822 |
0.00 % |
0 |
0.00 % |
822 |
0.01 % |
| q20,qd2,fs60,mq40 |
531 |
0.00 % |
0 |
0.00 % |
531 |
0.00 % |
| fs60,mq40 |
460 |
0.00 % |
0 |
0.00 % |
460 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
2778657 |
15.01 % |
| Transition |
G>A |
All |
5142739 |
27.79 % |
| Transition |
T>C |
All |
2648538 |
14.31 % |
| Transition |
C>T |
All |
5014786 |
27.09 % |
| Transversion |
A>C |
All |
205117 |
1.11 % |
| Transversion |
C>A |
All |
637125 |
3.44 % |
| Transversion |
T>G |
All |
217667 |
1.18 % |
| Transversion |
G>T |
All |
633952 |
3.43 % |
| Transversion |
A>T |
All |
438128 |
2.37 % |
| Transversion |
T>A |
All |
432472 |
2.34 % |
| Transversion |
C>G |
All |
183188 |
0.99 % |
| Transversion |
G>C |
All |
176603 |
0.95 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
331303 |
18.78 % |
| Transition |
G>A |
Passed |
306307 |
17.36 % |
| Transition |
T>C |
Passed |
330767 |
18.75 % |
| Transition |
C>T |
Passed |
306351 |
17.36 % |
| Transversion |
A>C |
Passed |
65366 |
3.70 % |
| Transversion |
C>A |
Passed |
59063 |
3.35 % |
| Transversion |
T>G |
Passed |
65418 |
3.71 % |
| Transversion |
G>T |
Passed |
59652 |
3.38 % |
| Transversion |
A>T |
Passed |
39587 |
2.24 % |
| Transversion |
T>A |
Passed |
39380 |
2.23 % |
| Transversion |
C>G |
Passed |
80767 |
4.58 % |
| Transversion |
G>C |
Passed |
80471 |
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 |
5.33 |
15584720 |
2924252 |
| Passed |
2.60 |
1274728 |
489704 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |