Search for Variation information by Variation ID:
Detailed information for vg0128724268:
| Variant ID: vg0128724268 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724268 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 45. )
Flanking Sequence (100 bp) in Reference Genome:
TTGTCTGCTGATGACGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGTCGCACGTCTGTCCTTCTTCAT[A/G]
CAATGACTTCTTTGCAATGGTTGCGATGAAGCCTGGAATGTATCTAGCCGGGACTGGCGTGCTAACTCCAGGAGTTAGCACACCGGCTCCGGCTAGGGAC
Reverse complement sequence
GTCCCTAGCCGGAGCCGGTGTGCTAACTCCTGGAGTTAGCACGCCAGTCCCGGCTAGATACATTCCAGGCTTCATCGCAACCATTGCAAAGAAGTCATTG[T/C]
ATGAAGAAGGACAGACGTGCGACATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATCAGCAGACAA
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 | 32.90% | 17.20% | 14.62% | 35.21% | NA |
| All Indica | 2759 | 5.30% | 27.80% | 16.56% | 50.34% | NA |
| All Japonica | 1512 | 85.40% | 0.50% | 1.92% | 12.17% | NA |
| Aus | 269 | 18.20% | 10.00% | 63.94% | 7.81% | NA |
| Indica I | 595 | 1.30% | 19.80% | 17.65% | 61.18% | NA |
| Indica II | 465 | 3.40% | 21.30% | 14.62% | 60.65% | NA |
| Indica III | 913 | 7.10% | 38.20% | 15.88% | 38.77% | NA |
| Indica Intermediate | 786 | 7.40% | 25.40% | 17.68% | 49.49% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 60.50% | 1.40% | 5.16% | 32.94% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 1.24% | 5.39% | NA |
| VI/Aromatic | 96 | 22.90% | 6.20% | 17.71% | 53.12% | NA |
| Intermediate | 90 | 52.20% | 8.90% | 17.78% | 21.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724268 | A -> G | LOC_Os01g49990.1 | missense_variant ; p.Tyr54Cys; MODERATE | nonsynonymous_codon ; Y54C | Average:13.84; most accessible tissue: Zhenshan97 panicle, score: 24.575 | probably damaging  |
3.257 |
DELETERIOUS | 0.03 |
| vg0128724268 | A -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:13.84; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0128724268 | NA | 9.46E-06 | mr1277 | 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 |
| vg0128724268 | NA | 2.50E-06 | mr1837 | 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 |