| Variant ID: vg0909153765 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 9153765 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, T: 0.01, others allele: 0.00, population size: 327. )
AGCTTTCTCTTTAGGACTGTTGTCCAAGCCTATCAATGAGCAAGACAATAAGGGTTTCCCAATTGTGCAATATGCAGATGATACCCTCATTCTGCTTAAG[T/G]
CTGACCAAAGAGAACTCTTCTGCTTTAAAGCAATTCTGAATACTTTTGCTCAATCCACAGGACTTAAGGTGAATTATCATAAGTCACAGCTTTACCCCCT
AGGGGGTAAAGCTGTGACTTATGATAATTCACCTTAAGTCCTGTGGATTGAGCAAAAGTATTCAGAATTGCTTTAAAGCAGAAGAGTTCTCTTTGGTCAG[A/C]
CTTAAGCAGAATGAGGGTATCATCTGCATATTGCACAATTGGGAAACCCTTATTGTCTTGCTCATTGATAGGCTTGGACAACAGTCCTAAAGAGAAAGCT
| 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 | 68.40% | 28.70% | 0.11% | 2.79% | NA |
| All Indica | 2759 | 94.40% | 4.70% | 0.11% | 0.83% | NA |
| All Japonica | 1512 | 18.80% | 76.80% | 0.13% | 4.23% | NA |
| Aus | 269 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.00% | 4.90% | 0.00% | 0.17% | NA |
| Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 91.70% | 6.40% | 0.11% | 1.86% | NA |
| Indica Intermediate | 786 | 94.40% | 4.70% | 0.25% | 0.64% | NA |
| Temperate Japonica | 767 | 22.40% | 73.80% | 0.13% | 3.65% | NA |
| Tropical Japonica | 504 | 7.30% | 88.30% | 0.00% | 4.37% | NA |
| Japonica Intermediate | 241 | 31.50% | 62.20% | 0.41% | 5.81% | NA |
| VI/Aromatic | 96 | 39.60% | 16.70% | 0.00% | 43.75% | NA |
| Intermediate | 90 | 50.00% | 46.70% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0909153765 | T -> G | LOC_Os09g15100.1 | missense_variant ; p.Ser171Ala; MODERATE | nonsynonymous_codon ; S171A | Average:51.776; most accessible tissue: Callus, score: 82.247 | unknown | unknown | TOLERATED | 1.00 |
| vg0909153765 | T -> DEL | LOC_Os09g15100.1 | N | frameshift_variant | Average:51.776; most accessible tissue: Callus, score: 82.247 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0909153765 | 6.68E-07 | 7.16E-42 | mr1480 | 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 |
| vg0909153765 | NA | 2.61E-09 | mr1705_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 |