Search for Variation information by Variation ID:
Detailed information for vg0615110843:
| Variant ID: vg0615110843 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 15110843 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CAGAGGCTAGGAAGAATTCTAGAAAGGTTAATCATGTATGTCCTTATATATATGGATCGGATGATGAGGATGATGTCTCTGAGATAGCTGCAGCCAGTGG[G/A]
TGAAGAACTCAGGGAAAGAGGAGAGGTATGACTTTGATATAACCAAGGCTGACAAAATTTTTGACTTGCTATTCCGAGAGAAGCAGATTCAACTTCCTAC
Reverse complement sequence
GTAGGAAGTTGAATCTGCTTCTCTCGGAATAGCAAGTCAAAAATTTTGTCAGCCTTGGTTATATCAAAGTCATACCTCTCCTCTTTCCCTGAGTTCTTCA[C/T]
CCACTGGCTGCAGCTATCTCAGAGACATCATCCTCATCATCCGATCCATATATATAAGGACATACATGATTAACCTTTCTAGAATTCTTCCTAGCCTCTG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 69.40% | 27.20% | 3.03% | 0.42% | NA |
| All Indica | 2759 | 56.10% | 40.10% | 3.81% | 0.00% | NA |
| All Japonica | 1512 | 92.30% | 7.60% | 0.00% | 0.07% | NA |
| Aus | 269 | 84.00% | 15.60% | 0.37% | 0.00% | NA |
| Indica I | 595 | 87.20% | 11.40% | 1.34% | 0.00% | NA |
| Indica II | 465 | 75.70% | 23.20% | 1.08% | 0.00% | NA |
| Indica III | 913 | 20.80% | 72.30% | 6.90% | 0.00% | NA |
| Indica Intermediate | 786 | 62.00% | 34.40% | 3.69% | 0.00% | NA |
| Temperate Japonica | 767 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 83.10% | 16.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 93.40% | 6.20% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 41.70% | 4.20% | 36.46% | 17.71% | NA |
| Intermediate | 90 | 75.60% | 20.00% | 2.22% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0615110843 | G -> A | LOC_Os06g25860.1 | missense_variant ; p.Val119Met; MODERATE | nonsynonymous_codon ; V119I | Average:36.315; most accessible tissue: Minghui63 flag leaf, score: 42.823 | benign  |
0.159 |
TOLERATED | 0.13 |
| vg0615110843 | G -> A | LOC_Os06g25860.1 | missense_variant ; p.Val119Met; MODERATE | nonsynonymous_codon ; V119M | Average:36.315; most accessible tissue: Minghui63 flag leaf, score: 42.823 | probably damaging |
2.163 |
DELETERIOUS | 0.04 |
| vg0615110843 | G -> DEL | LOC_Os06g25860.1 | N | frameshift_variant | Average:36.315; most accessible tissue: Minghui63 flag leaf, score: 42.823 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0615110843 | NA | 1.26E-10 | mr1087_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0615110843 | NA | 1.34E-10 | mr1234_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0615110843 | NA | 3.02E-06 | mr1623_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0615110843 | 7.93E-06 | 3.01E-08 | mr1734_2 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |