Search for Variation information by Variation ID:
Detailed information for vg0809871555:
| Variant ID: vg0809871555 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 9871555 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 286. )
Flanking Sequence (100 bp) in Reference Genome:
CTTCAGCAACTCAACCAACCCCACTGCATTTCAAGTACAACCCCATCGGCCCACCCGGAGGGGAATACAAGTCAAGGTGCGCCTAATTGGTTGCCACCGA[T/A]
TCAGCCGGGCCTGGGAGTTTCGCCGTGGAATCAAGGACCGCAGTTCGACTTCATCAACGCTGCTCAGGCGCCAACCGTTCGGCAGCAAGCTCCAACTCCA
Reverse complement sequence
TGGAGTTGGAGCTTGCTGCCGAACGGTTGGCGCCTGAGCAGCGTTGATGAAGTCGAACTGCGGTCCTTGATTCCACGGCGAAACTCCCAGGCCCGGCTGA[A/T]
TCGGTGGCAACCAATTAGGCGCACCTTGACTTGTATTCCCCTCCGGGTGGGCCGATGGGGTTGTACTTGAAATGCAGTGGGGTTGGTTGAGTTGCTGAAG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.00% | 8.80% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 85.10% | 14.70% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.10% | 0.37% | 0.00% | NA |
| Indica I | 595 | 96.00% | 4.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 91.80% | 8.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 73.90% | 25.60% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 85.80% | 14.00% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0809871555 | T -> A | LOC_Os08g16190.1 | missense_variant ; p.Ile254Asn; MODERATE | nonsynonymous_codon ; I254N | Average:53.969; most accessible tissue: Zhenshan97 flag leaf, score: 82.874 | possibly damaging  |
1.687 |
TOLERATED | 0.33 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0809871555 | NA | 9.91E-06 | mr1069 | 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 |
| vg0809871555 | 8.76E-06 | NA | mr1183 | 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 |
| vg0809871555 | NA | 9.99E-06 | mr1202 | 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 |
| vg0809871555 | 1.59E-06 | NA | mr1503 | 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 |
| vg0809871555 | 2.67E-06 | NA | mr1503 | 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 |
| vg0809871555 | NA | 3.11E-06 | mr1900_2 | 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 |