Search for Variation information by Variation ID:
Detailed information for vg0401635742:
| Variant ID: vg0401635742 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1635742 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.59, A: 0.41, others allele: 0.00, population size: 73. )
Flanking Sequence (100 bp) in Reference Genome:
GGAGGTCATTGAATTCTGCGTAGAATTTATTGAAGACCTTCACCCAATCGGGGTACCTGAATCACGCCATGAAGGGAGACTACGGGGAAAGGGGACTCTC[A/G]
GAAGGAAAGCAATAATGACGGTAGACAACAATTTATTCCGTAAAGCCCATTTCACGATTTTACAACAACCTTCATTGGTGGCTCCTTACATCGAGGAGCA
Reverse complement sequence
TGCTCCTCGATGTAAGGAGCCACCAATGAAGGTTGTTGTAAAATCGTGAAATGGGCTTTACGGAATAAATTGTTGTCTACCGTCATTATTGCTTTCCTTC[T/C]
GAGAGTCCCCTTTCCCCGTAGTCTCCCTTCATGGCGTGATTCAGGTACCCCGATTGGGTGAAGGTCTTCAATAAATTCTACGCAGAATTCAATGACCTCC
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 | 65.60% | 0.40% | 2.09% | 31.91% | NA |
| All Indica | 2759 | 74.00% | 0.10% | 1.05% | 24.79% | NA |
| All Japonica | 1512 | 49.70% | 0.30% | 2.58% | 47.49% | NA |
| Aus | 269 | 72.50% | 3.00% | 8.92% | 15.61% | NA |
| Indica I | 595 | 69.70% | 0.00% | 0.84% | 29.41% | NA |
| Indica II | 465 | 69.20% | 0.00% | 0.22% | 30.54% | NA |
| Indica III | 913 | 79.40% | 0.00% | 1.20% | 19.39% | NA |
| Indica Intermediate | 786 | 73.80% | 0.50% | 1.53% | 24.17% | NA |
| Temperate Japonica | 767 | 69.90% | 0.10% | 3.65% | 26.34% | NA |
| Tropical Japonica | 504 | 24.00% | 0.60% | 1.59% | 73.81% | NA |
| Japonica Intermediate | 241 | 39.00% | 0.00% | 1.24% | 59.75% | NA |
| VI/Aromatic | 96 | 53.10% | 4.20% | 7.29% | 35.42% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 0.00% | 33.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401635742 | A -> DEL | LOC_Os04g03700.1 | N | frameshift_variant | Average:7.568; most accessible tissue: Callus, score: 12.889 | N | N | N | N |
| vg0401635742 | A -> G | LOC_Os04g03700.1 | missense_variant ; p.Arg697Gly; MODERATE | nonsynonymous_codon ; R697G | Average:7.568; most accessible tissue: Callus, score: 12.889 | benign  |
-1.066 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401635742 | 4.47E-07 | NA | mr1064 | 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 |