Search for Variation information by Variation ID:
Detailed information for vg1005046900:
| Variant ID: vg1005046900 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 5046900 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 108. )
Flanking Sequence (100 bp) in Reference Genome:
TTCAACTAAGCCTCATGTTTTCGATGGAACGGATTTTTCTTATTGGTGTAGTAGGATGCAATCTTACATTATGTCTGAAAATTATGATATTTGGAGGAAA[G/A]
TTTCTCATCCTTATGTGATTCCTGAAGCCATTAATACTGATGCTTTAAAAACTGAATTTGAAAATAATTGCAAAGCTCGTAATATTCTTTTGAGTGGGAT
Reverse complement sequence
ATCCCACTCAAAAGAATATTACGAGCTTTGCAATTATTTTCAAATTCAGTTTTTAAAGCATCAGTATTAATGGCTTCAGGAATCACATAAGGATGAGAAA[C/T]
TTTCCTCCAAATATCATAATTTTCAGACATAATGTAAGATTGCATCCTACTACACCAATAAGAAAAATCCGTTCCATCGAAAACATGAGGCTTAGTTGAA
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 | 39.20% | 19.60% | 10.85% | 30.30% | NA |
| All Indica | 2759 | 23.80% | 32.20% | 14.61% | 29.32% | NA |
| All Japonica | 1512 | 70.30% | 0.90% | 4.76% | 24.01% | NA |
| Aus | 269 | 17.50% | 3.00% | 8.55% | 71.00% | NA |
| Indica I | 595 | 38.00% | 23.90% | 11.43% | 26.72% | NA |
| Indica II | 465 | 18.10% | 27.10% | 15.91% | 38.92% | NA |
| Indica III | 913 | 19.20% | 41.50% | 16.65% | 22.67% | NA |
| Indica Intermediate | 786 | 22.00% | 30.80% | 13.87% | 33.33% | NA |
| Temperate Japonica | 767 | 79.70% | 0.40% | 5.35% | 14.60% | NA |
| Tropical Japonica | 504 | 59.50% | 1.20% | 3.37% | 35.91% | NA |
| Japonica Intermediate | 241 | 63.10% | 2.10% | 5.81% | 29.05% | NA |
| VI/Aromatic | 96 | 44.80% | 4.20% | 6.25% | 44.79% | NA |
| Intermediate | 90 | 47.80% | 13.30% | 10.00% | 28.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1005046900 | G -> A | LOC_Os10g09350.1 | missense_variant ; p.Val109Ile; MODERATE | nonsynonymous_codon ; V109I | Average:8.918; most accessible tissue: Zhenshan97 root, score: 18.731 | benign  |
0.877 |
DELETERIOUS | 0.04 |
| vg1005046900 | G -> DEL | LOC_Os10g09350.1 | N | frameshift_variant | Average:8.918; most accessible tissue: Zhenshan97 root, score: 18.731 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1005046900 | 1.61E-06 | 1.61E-06 | mr1356_2 | 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 |