Search for Variation information by Variation ID:
Detailed information for vg0904000622:
| Variant ID: vg0904000622 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 4000622 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.75, G: 0.25, others allele: 0.00, population size: 97. )
Flanking Sequence (100 bp) in Reference Genome:
ATATCATCCTGGGATAACGGTGGTCTTGGGGTGGTCTTCTTCCGAGAACTCTATCTTCTGCTCAGACCACTTCATCTTGGGTGCAGCCCCCTGCCATGTC[A/G]
AGCAGACTTCATGTTCCACTTTCTTGTATTCTCGCTTGGAGGAGTACGTTGTGGAACCACCGAAGATGTGTGAGATGTGGAGGTCGGAGTCTGGATACGC
Reverse complement sequence
GCGTATCCAGACTCCGACCTCCACATCTCACACATCTTCGGTGGTTCCACAACGTACTCCTCCAAGCGAGAATACAAGAAAGTGGAACATGAAGTCTGCT[T/C]
GACATGGCAGGGGGCTGCACCCAAGATGAAGTGGTCTGAGCAGAAGATAGAGTTCTCGGAAGAAGACCACCCCAAGACCACCGTTATCCCAGGATGATAT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.70% | 10.10% | 27.17% | 0.00% | NA |
| All Indica | 2759 | 50.50% | 14.60% | 34.94% | 0.00% | NA |
| All Japonica | 1512 | 97.70% | 0.70% | 1.65% | 0.00% | NA |
| Aus | 269 | 9.30% | 9.70% | 81.04% | 0.00% | NA |
| Indica I | 595 | 24.90% | 29.40% | 45.71% | 0.00% | NA |
| Indica II | 465 | 44.50% | 8.40% | 47.10% | 0.00% | NA |
| Indica III | 913 | 77.50% | 8.10% | 14.35% | 0.00% | NA |
| Indica Intermediate | 786 | 42.00% | 14.50% | 43.51% | 0.00% | NA |
| Temperate Japonica | 767 | 98.80% | 0.10% | 1.04% | 0.00% | NA |
| Tropical Japonica | 504 | 97.20% | 1.00% | 1.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.00% | 1.70% | 3.32% | 0.00% | NA |
| VI/Aromatic | 96 | 11.50% | 34.40% | 54.17% | 0.00% | NA |
| Intermediate | 90 | 63.30% | 8.90% | 27.78% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0904000622 | A -> G | LOC_Os09g07870.1 | missense_variant ; p.Leu643Ser; MODERATE | nonsynonymous_codon ; L643S | Average:53.279; most accessible tissue: Zhenshan97 flag leaf, score: 79.935 | benign  |
-0.178 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0904000622 | NA | 1.59E-09 | mr1806 | 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 |
| vg0904000622 | NA | 8.40E-19 | mr1168_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 |
| vg0904000622 | NA | 6.53E-06 | mr1355_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 |
| vg0904000622 | NA | 1.93E-08 | mr1478_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 |
| vg0904000622 | NA | 2.86E-07 | mr1655_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 |