Search for Variation information by Variation ID:
Detailed information for vg0401800475:
| Variant ID: vg0401800475 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1800475 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.51, C: 0.49, others allele: 0.00, population size: 90. )
Flanking Sequence (100 bp) in Reference Genome:
ACCTCAGAAAGAAACGACTCAAGTTGCGGACACTCAAGACATAGCCATGATTGAAGCCGACTGGAGAGAGCCCCTCATACGATTTTTAACTTCTCAAGAA[T/C]
TCCCTCAAGATAAAGATGAAGCCGAGCGGATTTCAAGGCGTAGCAGGCTTTATGTTATTCATGAAGCCGAGTTATACAAGAAAAGCCCTTCAGGAATTCT
Reverse complement sequence
AGAATTCCTGAAGGGCTTTTCTTGTATAACTCGGCTTCATGAATAACATAAAGCCTGCTACGCCTTGAAATCCGCTCGGCTTCATCTTTATCTTGAGGGA[A/G]
TTCTTGAGAAGTTAAAAATCGTATGAGGGGCTCTCTCCAGTCGGCTTCAATCATGGCTATGTCTTGAGTGTCCGCAACTTGAGTCGTTTCTTTCTGAGGT
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 | 27.50% | 15.70% | 30.49% | 26.32% | NA |
| All Indica | 2759 | 28.30% | 2.40% | 39.94% | 29.32% | NA |
| All Japonica | 1512 | 27.20% | 43.60% | 7.08% | 22.09% | NA |
| Aus | 269 | 26.40% | 1.10% | 47.21% | 25.28% | NA |
| Indica I | 595 | 14.60% | 3.40% | 47.73% | 34.29% | NA |
| Indica II | 465 | 37.80% | 2.40% | 23.23% | 36.56% | NA |
| Indica III | 913 | 35.80% | 0.50% | 39.21% | 24.42% | NA |
| Indica Intermediate | 786 | 24.30% | 3.90% | 44.78% | 26.97% | NA |
| Temperate Japonica | 767 | 2.30% | 75.10% | 2.35% | 20.21% | NA |
| Tropical Japonica | 504 | 65.90% | 4.40% | 7.94% | 21.83% | NA |
| Japonica Intermediate | 241 | 25.70% | 25.30% | 20.33% | 28.63% | NA |
| VI/Aromatic | 96 | 12.50% | 0.00% | 79.17% | 8.33% | NA |
| Intermediate | 90 | 24.40% | 15.60% | 32.22% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401800475 | T -> C | LOC_Os04g03940.1 | missense_variant ; p.Phe1497Leu; MODERATE | nonsynonymous_codon ; F1497L | Average:20.062; most accessible tissue: Minghui63 young leaf, score: 31.294 | benign  |
-0.706 |
TOLERATED | 1.00 |
| vg0401800475 | T -> DEL | LOC_Os04g03940.1 | N | frameshift_variant | Average:20.062; most accessible tissue: Minghui63 young leaf, score: 31.294 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401800475 | NA | 3.01E-07 | mr1182 | 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 |
| vg0401800475 | NA | 3.26E-06 | mr1282 | 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 |
| vg0401800475 | NA | 6.22E-07 | mr1650 | 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 |
| vg0401800475 | 5.02E-06 | 2.65E-08 | mr1789 | Ind_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 |
| vg0401800475 | NA | 1.99E-07 | mr1693_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 |