Search for Variation information by Variation ID:
Detailed information for vg1208012170:
| Variant ID: vg1208012170 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 8012170 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )
Flanking Sequence (100 bp) in Reference Genome:
TTTCTCAATACTGTCAACCACCTTTAAACCGGGTATGAACTTCTTTAGCCAGTTCACCTGCCCCGTGGCCTCATAGCATGCTATAAACTCGACATACATA[G/A]
TAGACCCTCCAGTGATAGTCTGTTTTGAGCTTTTCCATGAAATAGCTCCTCCTGCAAGGGTGAACACGTATCCCGATGTTGACTTTGCATTATCTTTTGC
Reverse complement sequence
GCAAAAGATAATGCAAAGTCAACATCGGGATACGTGTTCACCCTTGCAGGAGGAGCTATTTCATGGAAAAGCTCAAAACAGACTATCACTGGAGGGTCTA[C/T]
TATGTATGTCGAGTTTATAGCATGCTATGAGGCCACGGGGCAGGTGAACTGGCTAAAGAAGTTCATACCCGGTTTAAAGGTGGTTGACAGTATTGAGAAA
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 | 82.30% | 5.90% | 1.50% | 10.30% | NA |
| All Indica | 2759 | 88.50% | 3.20% | 1.05% | 7.21% | NA |
| All Japonica | 1512 | 78.80% | 0.30% | 2.58% | 18.25% | NA |
| Aus | 269 | 34.20% | 65.40% | 0.00% | 0.37% | NA |
| Indica I | 595 | 80.50% | 5.00% | 3.36% | 11.09% | NA |
| Indica II | 465 | 93.10% | 1.50% | 0.00% | 5.38% | NA |
| Indica III | 913 | 91.10% | 2.10% | 0.44% | 6.35% | NA |
| Indica Intermediate | 786 | 88.80% | 4.20% | 0.64% | 6.36% | NA |
| Temperate Japonica | 767 | 79.80% | 0.30% | 1.56% | 18.38% | NA |
| Tropical Japonica | 504 | 88.90% | 0.20% | 2.78% | 8.13% | NA |
| Japonica Intermediate | 241 | 54.80% | 0.80% | 5.39% | 39.00% | NA |
| VI/Aromatic | 96 | 89.60% | 5.20% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 84.40% | 5.60% | 3.33% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1208012170 | G -> DEL | LOC_Os12g14120.1 | N | frameshift_variant | Average:42.691; most accessible tissue: Zhenshan97 flag leaf, score: 61.926 | N | N | N | N |
| vg1208012170 | G -> A | LOC_Os12g14120.1 | missense_variant ; p.Thr635Ile; MODERATE | nonsynonymous_codon ; T635I | Average:42.691; most accessible tissue: Zhenshan97 flag leaf, score: 61.926 | probably damaging  |
2.051 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208012170 | 4.68E-09 | NA | mr1244_2 | 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 |
| vg1208012170 | NA | 9.57E-06 | mr1265_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 |
| vg1208012170 | NA | 3.17E-06 | mr1977_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 |