Search for Variation information by Variation ID:
Detailed information for vg0130038156:
| Variant ID: vg0130038156 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 30038156 |
| 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: 318. )
Flanking Sequence (100 bp) in Reference Genome:
GAGAGTGGATAAGGCACCGACAGAACCAAATACTTGATGGAAGTGTGAATTGATGTACAGGATCACCTTTGCCACTGGAGCCATCTCTGCTGCTATATGG[A/G]
CAATGTGCAAGCCAGAACTGCATTGACTGATAATATATTAGAAAATACTAGCTAAAGGTCCGTGTGTTGTAATGGATATTACAAGAGATAAAAGCACAAG
Reverse complement sequence
CTTGTGCTTTTATCTCTTGTAATATCCATTACAACACACGGACCTTTAGCTAGTATTTTCTAATATATTATCAGTCAATGCAGTTCTGGCTTGCACATTG[T/C]
CCATATAGCAGCAGAGATGGCTCCAGTGGCAAAGGTGATCCTGTACATCAATTCACACTTCCATCAAGTATTTGGTTCTGTCGGTGCCTTATCCACTCTC
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 | 91.50% | 6.90% | 1.63% | 0.00% | NA |
| All Indica | 2759 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 77.10% | 18.00% | 4.89% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 68.70% | 23.60% | 7.69% | 0.00% | NA |
| Tropical Japonica | 504 | 88.90% | 10.50% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 79.30% | 15.80% | 4.98% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 15.60% | 3.33% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0130038156 | A -> G | LOC_Os01g52250.1 | missense_variant ; p.Val483Ala; MODERATE | nonsynonymous_codon ; V483A | Average:50.011; most accessible tissue: Minghui63 panicle, score: 62.157 | benign  |
0.245 |
TOLERATED | 0.07 |
| vg0130038156 | A -> G | LOC_Os01g52250.2 | missense_variant ; p.Val480Ala; MODERATE | nonsynonymous_codon ; V480A | Average:50.011; most accessible tissue: Minghui63 panicle, score: 62.157 | benign |
0.245 |
TOLERATED | 0.07 |
| vg0130038156 | A -> G | LOC_Os01g52250.4 | missense_variant ; p.Val480Ala; MODERATE | nonsynonymous_codon ; V480A | Average:50.011; most accessible tissue: Minghui63 panicle, score: 62.157 | benign |
0.245 |
TOLERATED | 0.07 |
| vg0130038156 | A -> G | LOC_Os01g52250.5 | missense_variant ; p.Val483Ala; MODERATE | nonsynonymous_codon ; V483A | Average:50.011; most accessible tissue: Minghui63 panicle, score: 62.157 | benign |
0.245 |
TOLERATED | 0.07 |
| vg0130038156 | A -> G | LOC_Os01g52250.6 | missense_variant ; p.Val483Ala; MODERATE | nonsynonymous_codon ; V483A | Average:50.011; most accessible tissue: Minghui63 panicle, score: 62.157 | benign |
0.296 |
TOLERATED | 0.07 |
| vg0130038156 | A -> G | LOC_Os01g52250.3 | missense_variant ; p.Val480Ala; MODERATE | nonsynonymous_codon ; V480A | Average:50.011; most accessible tissue: Minghui63 panicle, score: 62.157 | benign |
0.245 |
TOLERATED | 0.07 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0130038156 | 3.76E-06 | 3.76E-06 | mr1074_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 |
| vg0130038156 | NA | 1.47E-06 | mr1097_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 |
| vg0130038156 | NA | 2.04E-06 | mr1129_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 |
| vg0130038156 | NA | 7.57E-06 | mr1154_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 |
| vg0130038156 | NA | 1.19E-07 | mr1252_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 |
| vg0130038156 | NA | 3.70E-06 | mr1252_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 |
| vg0130038156 | NA | 9.19E-06 | mr1723_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 |