/EXTERNAL BLUEPRINT/variants/K006260_19_lane_gembs
BACK
SAMPLE K006260_19_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1148474248 |
918799252 |
80.00 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1148474248 |
100% |
1136183378 |
98.93 % |
12290870 |
1.07 % |
| |
|
|
|
|
|
|
| Passed |
920108969 |
80.12 % |
916792189 |
80.69 % |
3316780 |
0.36 % |
| Filtered |
228365279 |
19.88 % |
219391189 |
19.31 % |
8974090 |
0.98 % |
| |
|
|
|
|
|
|
| q20 |
182227845 |
79.80 % |
181188453 |
82.59 % |
1039392 |
11.58 % |
| q20,qd2 |
17141188 |
7.51 % |
9932818 |
4.53 % |
7208370 |
80.32 % |
| q20,mq40 |
14240027 |
6.24 % |
14123313 |
6.44 % |
116714 |
1.30 % |
| mq40 |
8984181 |
3.93 % |
8749765 |
3.99 % |
234416 |
2.61 % |
| q20,qd2,mq40 |
3004852 |
1.32 % |
2779169 |
1.27 % |
225683 |
2.51 % |
| qd2 |
2651687 |
1.16 % |
2524808 |
1.15 % |
126879 |
1.41 % |
| qd2,mq40 |
107576 |
0.05 % |
92863 |
0.04 % |
14713 |
0.16 % |
| q20,qd2,fs60 |
3034 |
0.00 % |
0 |
0.00 % |
3034 |
0.03 % |
| qd2,fs60,mq40 |
1509 |
0.00 % |
0 |
0.00 % |
1509 |
0.02 % |
| fs60 |
1307 |
0.00 % |
0 |
0.00 % |
1307 |
0.01 % |
| qd2,fs60 |
889 |
0.00 % |
0 |
0.00 % |
889 |
0.01 % |
| fs60,mq40 |
736 |
0.00 % |
0 |
0.00 % |
736 |
0.01 % |
| q20,qd2,fs60,mq40 |
441 |
0.00 % |
0 |
0.00 % |
441 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
2992614 |
20.94 % |
| Transition |
G>A |
All |
2971013 |
20.79 % |
| Transition |
T>C |
All |
2942363 |
20.59 % |
| Transition |
C>T |
All |
2897177 |
20.28 % |
| Transversion |
A>C |
All |
202818 |
1.42 % |
| Transversion |
C>A |
All |
479544 |
3.36 % |
| Transversion |
T>G |
All |
208449 |
1.46 % |
| Transversion |
G>T |
All |
478738 |
3.35 % |
| Transversion |
A>T |
All |
368162 |
2.58 % |
| Transversion |
T>A |
All |
354726 |
2.48 % |
| Transversion |
C>G |
All |
198663 |
1.39 % |
| Transversion |
G>C |
All |
194487 |
1.36 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
523317 |
17.55 % |
| Transition |
G>A |
Passed |
503467 |
16.89 % |
| Transition |
T>C |
Passed |
526025 |
17.64 % |
| Transition |
C>T |
Passed |
504755 |
16.93 % |
| Transversion |
A>C |
Passed |
119007 |
3.99 % |
| Transversion |
C>A |
Passed |
119288 |
4.00 % |
| Transversion |
T>G |
Passed |
118971 |
3.99 % |
| Transversion |
G>T |
Passed |
118861 |
3.99 % |
| Transversion |
A>T |
Passed |
94280 |
3.16 % |
| Transversion |
T>A |
Passed |
93892 |
3.15 % |
| Transversion |
C>G |
Passed |
129538 |
4.35 % |
| Transversion |
G>C |
Passed |
129890 |
4.36 % |
| |
|
|
|
|
| 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 |
4.75 |
11803167 |
2485587 |
| Passed |
2.23 |
2057564 |
923727 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |