Search for Variation information by Variation ID:
Detailed information for vg1218479048:
| Variant ID: vg1218479048 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18479048 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 97. )
Flanking Sequence (100 bp) in Reference Genome:
AAACATCACATCTTTATCAAACTTAGCAACCAAACAAGTTATCACAGGTGAAACAGAATTTTCAAAATCAGCTTTAAACACTCTTCCATAACGAGAAATA[T/G]
TCAGCACAGAATCACCACAAGAATCAAAAATTTTACTTCTAGTTTTCTTAAAGTGAACTTCAAACTCTTCATCAACAATTTGTGAAACCGAAAGCAAATT
Reverse complement sequence
AATTTGCTTTCGGTTTCACAAATTGTTGATGAAGAGTTTGAAGTTCACTTTAAGAAAACTAGAAGTAAAATTTTTGATTCTTGTGGTGATTCTGTGCTGA[A/C]
TATTTCTCGTTATGGAAGAGTGTTTAAAGCTGATTTTGAAAATTCTGTTTCACCTGTGATAACTTGTTTGGTTGCTAAGTTTGATAAAGATGTGATGTTT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 16.30% | 4.60% | 51.29% | 27.85% | NA |
| All Indica | 2759 | 5.90% | 6.30% | 69.23% | 18.63% | NA |
| All Japonica | 1512 | 36.20% | 1.50% | 14.62% | 47.75% | NA |
| Aus | 269 | 8.90% | 7.10% | 78.44% | 5.58% | NA |
| Indica I | 595 | 7.60% | 4.90% | 77.82% | 9.75% | NA |
| Indica II | 465 | 5.20% | 6.50% | 74.41% | 13.98% | NA |
| Indica III | 913 | 5.40% | 6.70% | 62.43% | 25.52% | NA |
| Indica Intermediate | 786 | 5.60% | 6.70% | 67.56% | 20.10% | NA |
| Temperate Japonica | 767 | 60.20% | 0.40% | 5.87% | 33.51% | NA |
| Tropical Japonica | 504 | 5.00% | 2.80% | 20.24% | 72.02% | NA |
| Japonica Intermediate | 241 | 24.90% | 2.10% | 30.71% | 42.32% | NA |
| VI/Aromatic | 96 | 8.30% | 1.00% | 41.67% | 48.96% | NA |
| Intermediate | 90 | 30.00% | 3.30% | 46.67% | 20.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218479048 | T -> DEL | LOC_Os12g30770.1 | N | frameshift_variant | Average:7.856; most accessible tissue: Minghui63 flag leaf, score: 12.43 | N | N | N | N |
| vg1218479048 | T -> G | LOC_Os12g30770.1 | missense_variant ; p.Asn89Thr; MODERATE | nonsynonymous_codon | Average:7.856; most accessible tissue: Minghui63 flag leaf, score: 12.43 | benign  |
1.255 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1218479048 | 2.54E-06 | NA | mr1745 | Jap_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 |