Search for Variation information by Variation ID:
Detailed information for vg0128647483:
| Variant ID: vg0128647483 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28647483 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 281. )
Flanking Sequence (100 bp) in Reference Genome:
TCATGCTATAACATGTTTAGGGTTGAGAGGCAACTGTTTAATAGGCTGCACAATATTTTGGTTGAGTCTTATGGGTTGCAGTCCACAACAAAAATGTCAT[C/T]
TGTAGAAGCTCTAGCCATTTTTTTGTGGATTGTTGGTGCACCACAGTCAATTAGACAGGCTGATGACCGTTTGGTTAGATCTTTGGAGACAATTAGCCGG
Reverse complement sequence
CCGGCTAATTGTCTCCAAAGATCTAACCAAACGGTCATCAGCCTGTCTAATTGACTGTGGTGCACCAACAATCCACAAAAAAATGGCTAGAGCTTCTACA[G/A]
ATGACATTTTTGTTGTGGACTGCAACCCATAAGACTCAACCAAAATATTGTGCAGCCTATTAAACAGTTGCCTCTCAACCCTAAACATGTTATAGCATGA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.90% | 3.70% | 3.60% | 14.81% | NA |
| All Indica | 2759 | 76.70% | 0.90% | 4.82% | 17.58% | NA |
| All Japonica | 1512 | 90.50% | 0.00% | 0.66% | 8.80% | NA |
| Aus | 269 | 33.50% | 40.10% | 4.83% | 21.56% | NA |
| Indica I | 595 | 89.10% | 0.00% | 3.53% | 7.39% | NA |
| Indica II | 465 | 56.10% | 0.60% | 12.69% | 30.54% | NA |
| Indica III | 913 | 76.90% | 0.50% | 1.42% | 21.14% | NA |
| Indica Intermediate | 786 | 79.30% | 2.20% | 5.09% | 13.49% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 74.40% | 0.00% | 1.19% | 24.40% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.00% | 1.24% | 3.32% | NA |
| VI/Aromatic | 96 | 28.10% | 37.50% | 12.50% | 21.88% | NA |
| Intermediate | 90 | 87.80% | 6.70% | 2.22% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128647483 | C -> T | LOC_Os01g49870.1 | missense_variant ; p.Ser328Phe; MODERATE | nonsynonymous_codon ; S328F | Average:34.072; most accessible tissue: Callus, score: 72.735 | possibly damaging  |
1.961 |
DELETERIOUS | 0.02 |
| vg0128647483 | C -> DEL | LOC_Os01g49870.1 | N | frameshift_variant | Average:34.072; most accessible tissue: Callus, score: 72.735 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0128647483 | NA | 6.18E-12 | mr1612 | 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 |
| vg0128647483 | NA | 3.54E-08 | 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 |
| vg0128647483 | NA | 6.10E-08 | mr1126_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 |
| vg0128647483 | NA | 2.47E-10 | mr1166_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 |
| vg0128647483 | NA | 4.58E-08 | mr1567_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 |
| vg0128647483 | NA | 4.89E-13 | mr1612_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 |
| vg0128647483 | NA | 8.39E-08 | mr1765_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 |