Search for Variation information by Variation ID:
Detailed information for vg0800164413:
| Variant ID: vg0800164413 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 164413 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 80. )
Flanking Sequence (100 bp) in Reference Genome:
TGCAAGGAAGTCATTGTATGAAGAAGGGCAGACGTGTAGCATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTC[G/A]
CGTCATCGGCAGACAACCGTGCTCCCACGATGCATCTGCCTCCGGTGGAGTGGAGGTAGGTATGACCCATCTCGTCGGATGGTCATTTGGATAGCAGCCA
Reverse complement sequence
TGGCTGCTATCCAAATGACCATCCGACGAGATGGGTCATACCTACCTCCACTCCACCGGAGGCAGATGCATCGTGGGAGCACGGTTGTCTGCCGATGACG[C/T]
GACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGCTACACGTCTGCCCTTCTTCATACAATGACTTCCTTGCA
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 | 32.30% | 2.40% | 17.16% | 48.12% | NA |
| All Indica | 2759 | 5.50% | 3.80% | 21.20% | 69.52% | NA |
| All Japonica | 1512 | 87.10% | 0.10% | 1.06% | 11.71% | NA |
| Aus | 269 | 2.60% | 1.50% | 69.89% | 26.02% | NA |
| Indica I | 595 | 12.30% | 3.20% | 11.09% | 73.45% | NA |
| Indica II | 465 | 1.70% | 7.10% | 21.72% | 69.46% | NA |
| Indica III | 913 | 2.50% | 2.60% | 25.41% | 69.44% | NA |
| Indica Intermediate | 786 | 6.00% | 3.70% | 23.66% | 66.67% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 0.13% | 2.74% | NA |
| Tropical Japonica | 504 | 71.20% | 0.40% | 2.98% | 25.40% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.00% | 0.00% | 11.62% | NA |
| VI/Aromatic | 96 | 15.60% | 1.00% | 10.42% | 72.92% | NA |
| Intermediate | 90 | 42.20% | 1.10% | 13.33% | 43.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0800164413 | G -> A | LOC_Os08g01250.1 | missense_variant ; p.Ala24Val; MODERATE | nonsynonymous_codon ; A24V | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
-0.179 |
TOLERATED | 1.00 |
| vg0800164413 | G -> DEL | LOC_Os08g01250.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0800164413 | NA | 6.56E-14 | mr1653 | 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 |
| vg0800164413 | NA | 5.26E-09 | mr1746 | 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 |