Search for Variation information by Variation ID:
Detailed information for vg0405835279:
| Variant ID: vg0405835279 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 5835279 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.87, G: 0.15, others allele: 0.00, population size: 82. )
Flanking Sequence (100 bp) in Reference Genome:
GGTTAACTCATCACAAACTGAGTCTGGCGGTTTGAAGAGACCCATAACATAAACGGGAATTGCTTGAATAACAGCTTTAATTAGCACCTCCTTACCCCCT[A/G]
TCGATAGGAAATTTTCACCCCACTGAACCAGACGTTTCAAGATTCTGCTCTGCATGGTTTGGAATTTCCCTTTGTACAGCCTTCCTTCCGGCATTGGGAA
Reverse complement sequence
TTCCCAATGCCGGAAGGAAGGCTGTACAAAGGGAAATTCCAAACCATGCAGAGCAGAATCTTGAAACGTCTGGTTCAGTGGGGTGAAAATTTCCTATCGA[T/C]
AGGGGGTAAGGAGGTGCTAATTAAAGCTGTTATTCAAGCAATTCCCGTTTATGTTATGGGTCTCTTCAAACCGCCAGACTCAGTTTGTGATGAGTTAACC
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 | 49.30% | 30.60% | 0.42% | 19.64% | NA |
| All Indica | 2759 | 76.40% | 6.60% | 0.43% | 16.53% | NA |
| All Japonica | 1512 | 2.60% | 80.00% | 0.33% | 17.06% | NA |
| Aus | 269 | 33.80% | 7.80% | 0.74% | 57.62% | NA |
| Indica I | 595 | 81.20% | 1.80% | 0.50% | 16.47% | NA |
| Indica II | 465 | 78.50% | 10.10% | 0.22% | 11.18% | NA |
| Indica III | 913 | 75.50% | 8.00% | 0.77% | 15.77% | NA |
| Indica Intermediate | 786 | 72.60% | 6.60% | 0.13% | 20.61% | NA |
| Temperate Japonica | 767 | 0.70% | 94.10% | 0.00% | 5.22% | NA |
| Tropical Japonica | 504 | 5.80% | 56.30% | 0.99% | 36.90% | NA |
| Japonica Intermediate | 241 | 2.50% | 84.20% | 0.00% | 13.28% | NA |
| VI/Aromatic | 96 | 51.00% | 4.20% | 0.00% | 44.79% | NA |
| Intermediate | 90 | 48.90% | 32.20% | 1.11% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0405835279 | A -> DEL | LOC_Os04g10740.1 | N | frameshift_variant | Average:11.727; most accessible tissue: Callus, score: 66.921 | N | N | N | N |
| vg0405835279 | A -> G | LOC_Os04g10740.1 | missense_variant ; p.Ile845Thr; MODERATE | nonsynonymous_codon ; I845T | Average:11.727; most accessible tissue: Callus, score: 66.921 | benign  |
-1.274 |
TOLERATED | 0.58 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0405835279 | 1.12E-06 | 1.04E-07 | mr1134 | 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 |
| vg0405835279 | NA | 1.27E-14 | mr1361 | 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 |
| vg0405835279 | 6.76E-07 | 9.91E-08 | mr1504 | 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 |
| vg0405835279 | NA | 9.82E-13 | mr1035_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 |
| vg0405835279 | NA | 1.39E-08 | mr1748_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 |