Search for Variation information by Variation ID:
Detailed information for vg0620080444:
| Variant ID: vg0620080444 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20080444 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, G: 0.03, C: 0.01, others allele: 0.00, population size: 68. )
Flanking Sequence (100 bp) in Reference Genome:
TGAATGTCTCGAGCATTGTGATCCACAGCATCTCTTTCTCCGAATCTGGGACAAAGCTCTCATGATCTCCGCGTGCCCTTGTTCTACGCCAGTACACCGT[A/C]
CTGACAGGCACGTTATCCCGCACAACCCAACCGCTGTGTTGTACGTAGTTCTTGGCTGCTTCCACCGGGGCACTAGGTCGGCCGTCTTCGTCCACTTCCA
Reverse complement sequence
TGGAAGTGGACGAAGACGGCCGACCTAGTGCCCCGGTGGAAGCAGCCAAGAACTACGTACAACACAGCGGTTGGGTTGTGCGGGATAACGTGCCTGTCAG[T/G]
ACGGTGTACTGGCGTAGAACAAGGGCACGCGGAGATCATGAGAGCTTTGTCCCAGATTCGGAGAAAGAGATGCTGTGGATCACAATGCTCGAGACATTCA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.20% | 17.30% | 0.53% | 7.00% | NA |
| All Indica | 2759 | 82.90% | 16.60% | 0.14% | 0.36% | NA |
| All Japonica | 1512 | 77.70% | 2.10% | 1.06% | 19.18% | NA |
| Aus | 269 | 1.50% | 98.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 86.40% | 13.60% | 0.00% | 0.00% | NA |
| Indica II | 465 | 84.10% | 14.40% | 0.00% | 1.51% | NA |
| Indica III | 913 | 78.30% | 21.40% | 0.22% | 0.11% | NA |
| Indica Intermediate | 786 | 85.00% | 14.50% | 0.25% | 0.25% | NA |
| Temperate Japonica | 767 | 88.00% | 1.20% | 0.78% | 10.04% | NA |
| Tropical Japonica | 504 | 74.80% | 4.00% | 1.19% | 20.04% | NA |
| Japonica Intermediate | 241 | 51.00% | 0.80% | 1.66% | 46.47% | NA |
| VI/Aromatic | 96 | 17.70% | 53.10% | 4.17% | 25.00% | NA |
| Intermediate | 90 | 75.60% | 15.60% | 1.11% | 7.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620080444 | A -> C | LOC_Os06g34500.1 | missense_variant ; p.Ser34Arg; MODERATE | nonsynonymous_codon ; S34R | Average:33.48; most accessible tissue: Minghui63 young leaf, score: 65.161 | possibly damaging  |
1.97 |
DELETERIOUS | 0.00 |
| vg0620080444 | A -> DEL | LOC_Os06g34500.1 | N | frameshift_variant | Average:33.48; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0620080444 | NA | 3.51E-06 | mr1211 | 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 |
| vg0620080444 | NA | 7.78E-07 | mr1706 | 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 |
| vg0620080444 | NA | 6.90E-07 | mr1121_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 |
| vg0620080444 | NA | 2.92E-07 | mr1211_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 |
| vg0620080444 | 4.63E-06 | 4.84E-07 | mr1525_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 |
| vg0620080444 | NA | 1.50E-06 | mr1929_2 | 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 |