/EXTERNAL BLUEPRINT/variants/K006362_15_lane_gembs
BACK
SAMPLE K006362_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1078738167 |
545539770 |
50.57 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1078738167 |
100% |
1062213409 |
98.47 % |
16524758 |
1.53 % |
| |
|
|
|
|
|
|
| Passed |
547056143 |
50.71 % |
544461735 |
51.26 % |
2594408 |
0.47 % |
| Filtered |
531682024 |
49.29 % |
517751674 |
48.74 % |
13930350 |
2.55 % |
| |
|
|
|
|
|
|
| q20 |
443535290 |
83.42 % |
442021724 |
85.37 % |
1513566 |
10.87 % |
| q20,qd2 |
61395770 |
11.55 % |
49465852 |
9.55 % |
11929918 |
85.64 % |
| q20,mq40 |
14689988 |
2.76 % |
14599704 |
2.82 % |
90284 |
0.65 % |
| mq40 |
6061100 |
1.14 % |
5921068 |
1.14 % |
140032 |
1.01 % |
| q20,qd2,mq40 |
3337723 |
0.63 % |
3176323 |
0.61 % |
161400 |
1.16 % |
| qd2 |
2572076 |
0.48 % |
2497498 |
0.48 % |
74578 |
0.54 % |
| qd2,mq40 |
80607 |
0.02 % |
69505 |
0.01 % |
11102 |
0.08 % |
| q20,qd2,fs60 |
3087 |
0.00 % |
0 |
0.00 % |
3087 |
0.02 % |
| qd2,fs60 |
1927 |
0.00 % |
0 |
0.00 % |
1927 |
0.01 % |
| fs60 |
1910 |
0.00 % |
0 |
0.00 % |
1910 |
0.01 % |
| qd2,fs60,mq40 |
1405 |
0.00 % |
0 |
0.00 % |
1405 |
0.01 % |
| q20,qd2,fs60,mq40 |
690 |
0.00 % |
0 |
0.00 % |
690 |
0.00 % |
| fs60,mq40 |
449 |
0.00 % |
0 |
0.00 % |
449 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
2740135 |
11.75 % |
| Transition |
G>A |
All |
7798430 |
33.44 % |
| Transition |
T>C |
All |
2573161 |
11.03 % |
| Transition |
C>T |
All |
7613412 |
32.65 % |
| Transversion |
A>C |
All |
219814 |
0.94 % |
| Transversion |
C>A |
All |
482046 |
2.07 % |
| Transversion |
T>G |
All |
231405 |
0.99 % |
| Transversion |
G>T |
All |
471735 |
2.02 % |
| Transversion |
A>T |
All |
407081 |
1.75 % |
| Transversion |
T>A |
All |
409529 |
1.76 % |
| Transversion |
C>G |
All |
188979 |
0.81 % |
| Transversion |
G>C |
All |
182613 |
0.78 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
309053 |
19.13 % |
| Transition |
G>A |
Passed |
278937 |
17.26 % |
| Transition |
T>C |
Passed |
308503 |
19.09 % |
| Transition |
C>T |
Passed |
278964 |
17.27 % |
| Transversion |
A>C |
Passed |
59225 |
3.67 % |
| Transversion |
C>A |
Passed |
52113 |
3.23 % |
| Transversion |
T>G |
Passed |
58437 |
3.62 % |
| Transversion |
G>T |
Passed |
52279 |
3.24 % |
| Transversion |
A>T |
Passed |
34234 |
2.12 % |
| Transversion |
T>A |
Passed |
34029 |
2.11 % |
| Transversion |
C>G |
Passed |
74835 |
4.63 % |
| Transversion |
G>C |
Passed |
75069 |
4.65 % |
| |
|
|
|
|
| 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 |
7.99 |
20725138 |
2593202 |
| Passed |
2.67 |
1175457 |
440221 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |