Search for Variation information by Variation ID:
Detailed information for vg0819963368:
| Variant ID: vg0819963368 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 19963368 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.05, others allele: 0.00, population size: 55. )
Flanking Sequence (100 bp) in Reference Genome:
AGCCGAAGCCCTAGAATCAAAGAAACAATTTCCCTTGGGCAAAATCCTCCTCGGCTATCTATACCAAATGTTGAATAACGCATCGGCCAAGATAGCCGTC[A/G]
GCTCAGTAGTTGGGGCAGGTGGACCATGGTGGTTGCTGCAAACTTGGCTAAACTTGGTAGTTATGAAAGTCGTCAATTGGCCATCTGTGACAGAAGCTGA
Reverse complement sequence
TCAGCTTCTGTCACAGATGGCCAATTGACGACTTTCATAACTACCAAGTTTAGCCAAGTTTGCAGCAACCACCATGGTCCACCTGCCCCAACTACTGAGC[T/C]
GACGGCTATCTTGGCCGATGCGTTATTCAACATTTGGTATAGATAGCCGAGGAGGATTTTGCCCAAGGGAAATTGTTTCTTTGATTCTAGGGCTTCGGCT
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 | 56.60% | 15.20% | 11.36% | 16.84% | NA |
| All Indica | 2759 | 66.90% | 1.60% | 14.24% | 17.33% | NA |
| All Japonica | 1512 | 49.10% | 42.60% | 0.66% | 7.61% | NA |
| Aus | 269 | 9.70% | 1.50% | 30.48% | 58.36% | NA |
| Indica I | 595 | 31.30% | 1.20% | 22.02% | 45.55% | NA |
| Indica II | 465 | 86.00% | 2.80% | 1.94% | 9.25% | NA |
| Indica III | 913 | 78.80% | 0.90% | 15.66% | 4.71% | NA |
| Indica Intermediate | 786 | 68.70% | 1.90% | 13.99% | 15.39% | NA |
| Temperate Japonica | 767 | 37.90% | 61.40% | 0.39% | 0.26% | NA |
| Tropical Japonica | 504 | 72.00% | 9.10% | 0.79% | 18.06% | NA |
| Japonica Intermediate | 241 | 36.90% | 52.70% | 1.24% | 9.13% | NA |
| VI/Aromatic | 96 | 30.20% | 5.20% | 41.67% | 22.92% | NA |
| Intermediate | 90 | 36.70% | 23.30% | 13.33% | 26.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0819963368 | A -> G | LOC_Os08g32190.1 | missense_variant ; p.Ser203Gly; MODERATE | nonsynonymous_codon ; S203G | Average:15.367; most accessible tissue: Zhenshan97 flag leaf, score: 21.748 | benign  |
-0.704 |
TOLERATED | 1.00 |
| vg0819963368 | A -> DEL | LOC_Os08g32190.1 | N | frameshift_variant | Average:15.367; most accessible tissue: Zhenshan97 flag leaf, score: 21.748 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0819963368 | NA | 7.25E-07 | mr1805 | Jap_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 |
| vg0819963368 | NA | 6.31E-07 | mr1904 | 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 |
| vg0819963368 | NA | 1.23E-07 | mr1989 | 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 |
| vg0819963368 | NA | 1.24E-06 | mr1228_2 | Jap_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 |
| vg0819963368 | 2.01E-06 | 2.24E-11 | mr1551_2 | 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 |