Search for Variation information by Variation ID:
Detailed information for vg0815306355:
| Variant ID: vg0815306355 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 15306355 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 204. )
Flanking Sequence (100 bp) in Reference Genome:
AAGGTGATTAGCTTTCTAGATGGTAATGCCGGCTACAATAAAATCTTTATGGCGGAAGAGGATATGTACAAGACGGCTTTTAGGTGTCCGGGATTTGTTG[G/A]
TTTGTTTGAGTGGGTTGTCATGACTTTTGGGTTGAAGAACGCCGGTGCAACGTATCAAAGGGCAATGAATTTGATCTTCCATGATTTGCTAGGCATTATC
Reverse complement sequence
GATAATGCCTAGCAAATCATGGAAGATCAAATTCATTGCCCTTTGATACGTTGCACCGGCGTTCTTCAACCCAAAAGTCATGACAACCCACTCAAACAAA[C/T]
CAACAAATCCCGGACACCTAAAAGCCGTCTTGTACATATCCTCTTCCGCCATAAAGATTTTATTGTAGCCGGCATTACCATCTAGAAAGCTAATCACCTT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 46.50% | 39.00% | 7.26% | 7.28% | NA |
| All Indica | 2759 | 71.80% | 15.50% | 4.64% | 8.05% | NA |
| All Japonica | 1512 | 1.70% | 77.40% | 13.56% | 7.34% | NA |
| Aus | 269 | 56.10% | 38.70% | 1.49% | 3.72% | NA |
| Indica I | 595 | 88.20% | 0.50% | 6.05% | 5.21% | NA |
| Indica II | 465 | 70.10% | 12.00% | 4.73% | 13.12% | NA |
| Indica III | 913 | 63.20% | 24.80% | 4.05% | 8.00% | NA |
| Indica Intermediate | 786 | 70.50% | 18.10% | 4.20% | 7.25% | NA |
| Temperate Japonica | 767 | 2.00% | 61.90% | 23.60% | 12.52% | NA |
| Tropical Japonica | 504 | 1.20% | 96.60% | 0.79% | 1.39% | NA |
| Japonica Intermediate | 241 | 1.70% | 86.70% | 8.30% | 3.32% | NA |
| VI/Aromatic | 96 | 7.30% | 89.60% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 34.40% | 61.10% | 3.33% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0815306355 | G -> A | LOC_Os08g25190.1 | missense_variant ; p.Gly737Asp; MODERATE | nonsynonymous_codon ; G737D | Average:26.702; most accessible tissue: Minghui63 young leaf, score: 42.042 | benign  |
0.864 |
TOLERATED | 0.06 |
| vg0815306355 | G -> DEL | LOC_Os08g25190.1 | N | frameshift_variant | Average:26.702; most accessible tissue: Minghui63 young leaf, score: 42.042 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0815306355 | 7.45E-06 | 1.75E-16 | mr1484 | 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 |
| vg0815306355 | 2.83E-08 | 1.30E-09 | mr1484 | 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 |