Search for Variation information by Variation ID:
Detailed information for vg0323900305:
| Variant ID: vg0323900305 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 23900305 |
| 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, A: 0.02, others allele: 0.00, population size: 117. )
Flanking Sequence (100 bp) in Reference Genome:
GATGAGGCTGCAGCCGGGGACCTTGTCGATCTCGTTCCTCCTCATCTGCCTCCTCACCTTCACCGCCTCGCCGTGCCGGCCATTCGACGTGTACGTGTTC[G/A]
ACATCAACACGTAGTCGCCGGCGTCTGCGTCGGCGTCGGTGGTGCGCCGCCGCATCACCCGCTCGGCGCGCTCGACGTCACCGTGCGCGCGGCATGCGAC
Reverse complement sequence
GTCGCATGCCGCGCGCACGGTGACGTCGAGCGCGCCGAGCGGGTGATGCGGCGGCGCACCACCGACGCCGACGCAGACGCCGGCGACTACGTGTTGATGT[C/T]
GAACACGTACACGTCGAATGGCCGGCACGGCGAGGCGGTGAAGGTGAGGAGGCAGATGAGGAGGAACGAGATCGACAAGGTCCCCGGCTGCAGCCTCATC
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 | 94.60% | 5.40% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 90.80% | 9.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 72.40% | 27.60% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 90.30% | 9.70% | 0.00% | 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 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0323900305 | G -> A | LOC_Os03g42860.1 | missense_variant ; p.Ser79Leu; MODERATE | nonsynonymous_codon ; S79L | Average:58.224; most accessible tissue: Zhenshan97 panicle, score: 72.468 | possibly damaging  |
1.521 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0323900305 | NA | 5.64E-11 | Spikelet_length | Ind_All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0323900305 | NA | 4.71E-06 | mr1215 | 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 |