/EXTERNAL BLUEPRINT/variants/K006351_9_lane_gembs
BACK
SAMPLE K006351_9_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1100225324 |
610754703 |
55.51 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1100225324 |
100% |
1084497564 |
98.57 % |
15727760 |
1.43 % |
| |
|
|
|
|
|
|
| Passed |
612287721 |
55.65 % |
609497579 |
56.20 % |
2790142 |
0.46 % |
| Filtered |
487937603 |
44.35 % |
474999985 |
43.80 % |
12937618 |
2.11 % |
| |
|
|
|
|
|
|
| q20 |
411855911 |
84.41 % |
410334592 |
86.39 % |
1521319 |
11.76 % |
| q20,qd2 |
50150999 |
10.28 % |
39270935 |
8.27 % |
10880064 |
84.10 % |
| q20,mq40 |
14491533 |
2.97 % |
14386973 |
3.03 % |
104560 |
0.81 % |
| mq40 |
6235328 |
1.28 % |
6083103 |
1.28 % |
152225 |
1.18 % |
| q20,qd2,mq40 |
3283759 |
0.67 % |
3096851 |
0.65 % |
186908 |
1.44 % |
| qd2 |
1832282 |
0.38 % |
1757266 |
0.37 % |
75016 |
0.58 % |
| qd2,mq40 |
81269 |
0.02 % |
70265 |
0.01 % |
11004 |
0.09 % |
| q20,qd2,fs60 |
2033 |
0.00 % |
0 |
0.00 % |
2033 |
0.02 % |
| fs60 |
1339 |
0.00 % |
0 |
0.00 % |
1339 |
0.01 % |
| qd2,fs60,mq40 |
1203 |
0.00 % |
0 |
0.00 % |
1203 |
0.01 % |
| qd2,fs60 |
834 |
0.00 % |
0 |
0.00 % |
834 |
0.01 % |
| q20,qd2,fs60,mq40 |
596 |
0.00 % |
0 |
0.00 % |
596 |
0.00 % |
| fs60,mq40 |
516 |
0.00 % |
0 |
0.00 % |
516 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
2875580 |
15.44 % |
| Transition |
G>A |
All |
5137278 |
27.59 % |
| Transition |
T>C |
All |
2747850 |
14.76 % |
| Transition |
C>T |
All |
4993478 |
26.82 % |
| Transversion |
A>C |
All |
226794 |
1.22 % |
| Transversion |
C>A |
All |
572045 |
3.07 % |
| Transversion |
T>G |
All |
237587 |
1.28 % |
| Transversion |
G>T |
All |
566493 |
3.04 % |
| Transversion |
A>T |
All |
444881 |
2.39 % |
| Transversion |
T>A |
All |
439556 |
2.36 % |
| Transversion |
C>G |
All |
191789 |
1.03 % |
| Transversion |
G>C |
All |
185309 |
1.00 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
351244 |
18.83 % |
| Transition |
G>A |
Passed |
320145 |
17.16 % |
| Transition |
T>C |
Passed |
350081 |
18.76 % |
| Transition |
C>T |
Passed |
319432 |
17.12 % |
| Transversion |
A>C |
Passed |
70797 |
3.79 % |
| Transversion |
C>A |
Passed |
63432 |
3.40 % |
| Transversion |
T>G |
Passed |
70830 |
3.80 % |
| Transversion |
G>T |
Passed |
63651 |
3.41 % |
| Transversion |
A>T |
Passed |
43154 |
2.31 % |
| Transversion |
T>A |
Passed |
43024 |
2.31 % |
| Transversion |
C>G |
Passed |
84657 |
4.54 % |
| Transversion |
G>C |
Passed |
85314 |
4.57 % |
| |
|
|
|
|
| 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 |
5.50 |
15754186 |
2864454 |
| Passed |
2.55 |
1340902 |
524859 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |