Search for Variation information by Variation ID:
Detailed information for vg0714404540:
| Variant ID: vg0714404540 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14404540 |
| 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: 42. )
Flanking Sequence (100 bp) in Reference Genome:
TTCCTCGGACTTGGAGTAGATAAGTATGTCATCGATCAAAACCACTACAAACTTGTCTAGAAATTCCATAAACACCTTGTTCATCAAATTCATGAAGAAG[G/A]
CAGGTGCATTAGTGAGTCCGAAAGACATAACTGTGCATTCGAACAACCCATACCGAGTGATGAATGTTGTCTTTGGAATATCCTCTTCACGGATACTCAA
Reverse complement sequence
TTGAGTATCCGTGAAGAGGATATTCCAAAGACAACATTCATCACTCGGTATGGGTTGTTCGAATGCACAGTTATGTCTTTCGGACTCACTAATGCACCTG[C/T]
CTTCTTCATGAATTTGATGAACAAGGTGTTTATGGAATTTCTAGACAAGTTTGTAGTGGTTTTGATCGATGACATACTTATCTACTCCAAGTCCGAGGAA
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 | 72.30% | 3.70% | 13.44% | 10.58% | NA |
| All Indica | 2759 | 58.10% | 5.60% | 20.08% | 16.24% | NA |
| All Japonica | 1512 | 96.50% | 0.00% | 2.05% | 1.46% | NA |
| Aus | 269 | 70.30% | 6.30% | 14.87% | 8.55% | NA |
| Indica I | 595 | 76.00% | 4.20% | 14.96% | 4.87% | NA |
| Indica II | 465 | 57.40% | 7.30% | 21.08% | 14.19% | NA |
| Indica III | 913 | 41.80% | 6.40% | 25.08% | 26.73% | NA |
| Indica Intermediate | 786 | 63.90% | 4.70% | 17.56% | 13.87% | NA |
| Temperate Japonica | 767 | 97.00% | 0.00% | 1.17% | 1.83% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.79% | 0.20% | NA |
| Japonica Intermediate | 241 | 89.60% | 0.00% | 7.47% | 2.90% | NA |
| VI/Aromatic | 96 | 87.50% | 4.20% | 5.21% | 3.12% | NA |
| Intermediate | 90 | 88.90% | 1.10% | 5.56% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714404540 | G -> DEL | LOC_Os07g25210.1 | N | frameshift_variant | Average:9.852; most accessible tissue: Callus, score: 44.459 | N | N | N | N |
| vg0714404540 | G -> A | LOC_Os07g25210.1 | missense_variant ; p.Ala1031Val; MODERATE | nonsynonymous_codon ; A1031V | Average:9.852; most accessible tissue: Callus, score: 44.459 | benign  |
0.978 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714404540 | 4.69E-06 | 4.69E-06 | mr1462 | 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 |