Search for Variation information by Variation ID:
Detailed information for vg0317032441:
| Variant ID: vg0317032441 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17032441 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.64, G: 0.36, others allele: 0.00, population size: 101. )
Flanking Sequence (100 bp) in Reference Genome:
TATCTGGCCCCGATACTTTCCAGTCAAGAATGTCCCATCAATGCAGAGAACAGGACGACAGTTCACGAATGCCATCTTGCATGCATGTAGAGCTAAGAAC[A/G]
CCCTTTGCAGCACACTCTTGCCAGGATGTTCAATTGAGGGGAATTTCTTCACCGCGTAAGAGCTCCCAGGGTTTCTTTCTTCGATAACACCAAGCAGGCA
Reverse complement sequence
TGCCTGCTTGGTGTTATCGAAGAAAGAAACCCTGGGAGCTCTTACGCGGTGAAGAAATTCCCCTCAATTGAACATCCTGGCAAGAGTGTGCTGCAAAGGG[T/C]
GTTCTTAGCTCTACATGCATGCAAGATGGCATTCGTGAACTGTCGTCCTGTTCTCTGCATTGATGGGACATTCTTGACTGGAAAGTATCGGGGCCAGATA
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 | 58.30% | 39.70% | 0.23% | 1.82% | NA |
| All Indica | 2759 | 85.80% | 13.80% | 0.25% | 0.18% | NA |
| All Japonica | 1512 | 4.10% | 95.60% | 0.07% | 0.20% | NA |
| Aus | 269 | 98.10% | 1.50% | 0.00% | 0.37% | NA |
| Indica I | 595 | 97.80% | 2.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 86.90% | 13.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 77.80% | 21.70% | 0.11% | 0.44% | NA |
| Indica Intermediate | 786 | 85.40% | 13.90% | 0.64% | 0.13% | NA |
| Temperate Japonica | 767 | 0.30% | 99.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 11.70% | 88.10% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.40% | 98.30% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 16.70% | 8.30% | 0.00% | 75.00% | NA |
| Intermediate | 90 | 50.00% | 41.10% | 3.33% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317032441 | A -> DEL | LOC_Os03g29900.1 | N | frameshift_variant | Average:36.7; most accessible tissue: Minghui63 flag leaf, score: 62.47 | N | N | N | N |
| vg0317032441 | A -> G | LOC_Os03g29900.1 | missense_variant ; p.Val490Ala; MODERATE | nonsynonymous_codon ; V490A | Average:36.7; most accessible tissue: Minghui63 flag leaf, score: 62.47 | benign  |
-0.135 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0317032441 | NA | 5.07E-10 | Grain_weight | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0317032441 | 4.72E-06 | NA | mr1180 | 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 |
| vg0317032441 | NA | 4.59E-07 | mr1180 | Ind_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 |
| vg0317032441 | NA | 4.48E-10 | mr1307 | 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 |
| vg0317032441 | NA | 3.74E-17 | mr1557 | 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 |
| vg0317032441 | NA | 5.47E-07 | mr1646 | 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 |