Search for Variation information by Variation ID:
Detailed information for vg0524512577:
| Variant ID: vg0524512577 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 24512577 |
| 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: 359. )
Flanking Sequence (100 bp) in Reference Genome:
AACATAAATTCATCAGTATTGTACAAATTGTGCCTCCATCATCATCATCATCATCATCAGAATCATTGTCATTACATTACATCAATCAGTATCAGTTTTC[T/A]
CATCATCAGAGTCATCAGGACCAGTCGGTCGAAGATCGGTGTCCTGGAATCTCTCCACTACATCAACTGCTATCTTGTCAGCAACCTTCTGTGCATCATT
Reverse complement sequence
AATGATGCACAGAAGGTTGCTGACAAGATAGCAGTTGATGTAGTGGAGAGATTCCAGGACACCGATCTTCGACCGACTGGTCCTGATGACTCTGATGATG[A/T]
GAAAACTGATACTGATTGATGTAATGTAATGACAATGATTCTGATGATGATGATGATGATGATGGAGGCACAATTTGTACAATACTGATGAATTTATGTT
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 | 97.00% | 2.10% | 0.97% | 0.00% | NA |
| All Indica | 2759 | 94.90% | 3.50% | 1.63% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 83.00% | 10.90% | 6.05% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.90% | 1.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 96.20% | 2.80% | 1.02% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0524512577 | T -> A | LOC_Os05g41860.1 | missense_variant ; p.Glu739Val; MODERATE | nonsynonymous_codon ; E739V | Average:29.212; most accessible tissue: Minghui63 flag leaf, score: 42.036 | possibly damaging  |
1.954 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0524512577 | 2.17E-06 | 2.17E-06 | mr1035_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 |