Search for Variation information by Variation ID:
Detailed information for vg0623760476:
| Variant ID: vg0623760476 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 23760476 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 354. )
Flanking Sequence (100 bp) in Reference Genome:
GGATCTACTCAAGAGATTTGGCTTGGAGGATGCGAAGCCCATCAAGACACCTATGGCAACCAACGGGCATCTCGACCTTGATGAGGGAGGTAAACCGGTA[G/T]
ATTTAAAGCTTTATCGTTCTATGATTGGTAGCTTGCTTTATCTTACCGCATCTAGGCCGGATATCATGTTTAGTGTTTGCATGTGTGCACGGTTTCAAGC
Reverse complement sequence
GCTTGAAACCGTGCACACATGCAAACACTAAACATGATATCCGGCCTAGATGCGGTAAGATAAAGCAAGCTACCAATCATAGAACGATAAAGCTTTAAAT[C/A]
TACCGGTTTACCTCCCTCATCAAGGTCGAGATGCCCGTTGGTTGCCATAGGTGTCTTGATGGGCTTCGCATCCTCCAAGCCAAATCTCTTGAGTAGATCC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.70% | 14.20% | 1.08% | 0.08% | NA |
| All Indica | 2759 | 95.50% | 4.30% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 61.50% | 35.40% | 2.84% | 0.26% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 94.00% | 6.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 93.20% | 6.60% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 95.50% | 4.10% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 85.30% | 14.00% | 0.78% | 0.00% | NA |
| Tropical Japonica | 504 | 17.50% | 75.20% | 6.55% | 0.79% | NA |
| Japonica Intermediate | 241 | 78.00% | 20.30% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 15.60% | 3.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0623760476 | G -> T | LOC_Os06g39950.1 | missense_variant ; p.Asp65Tyr; MODERATE | nonsynonymous_codon ; D65Y | Average:38.774; most accessible tissue: Minghui63 flag leaf, score: 69.681 | probably damaging  |
2.805 |
DELETERIOUS | 0.00 |
| vg0623760476 | G -> DEL | LOC_Os06g39950.1 | N | frameshift_variant | Average:38.774; most accessible tissue: Minghui63 flag leaf, score: 69.681 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0623760476 | 7.93E-06 | NA | mr1103_2 | 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 |
| vg0623760476 | 1.94E-07 | NA | mr1264_2 | 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 |
| vg0623760476 | NA | 1.94E-08 | mr1408_2 | 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 |