| Variant ID: vg0216594509 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 16594509 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 126. )
CAGTATCAACCCACCAATTAGTAGACTAATTAACTGAAAAAACAGTTGCTAAATTACCATACTGCTTCCATCTCCAGTGTTGCCAATGGTCACATTAGCA[A/G]
ACTTAGAGGTCTGCCCTACAGGTGCCTTCATCCCCTTGCGTTGTGGACACTTCCTGGCCAGATGGCCAGGTTGACCACACACAAAGCAAGTCCTCTCATC
GATGAGAGGACTTGCTTTGTGTGTGGTCAACCTGGCCATCTGGCCAGGAAGTGTCCACAACGCAAGGGGATGAAGGCACCTGTAGGGCAGACCTCTAAGT[T/C]
TGCTAATGTGACCATTGGCAACACTGGAGATGGAAGCAGTATGGTAATTTAGCAACTGTTTTTTCAGTTAATTAGTCTACTAATTGGTGGGTTGATACTG
| 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 | 18.90% | 11.40% | 32.27% | 37.52% | NA |
| All Indica | 2759 | 7.00% | 1.10% | 46.68% | 45.23% | NA |
| All Japonica | 1512 | 37.20% | 33.10% | 7.28% | 22.49% | NA |
| Aus | 269 | 5.90% | 0.40% | 36.06% | 57.62% | NA |
| Indica I | 595 | 2.90% | 1.00% | 49.58% | 46.55% | NA |
| Indica II | 465 | 11.00% | 0.90% | 58.71% | 29.46% | NA |
| Indica III | 913 | 8.80% | 0.90% | 33.30% | 57.06% | NA |
| Indica Intermediate | 786 | 5.90% | 1.40% | 52.93% | 39.82% | NA |
| Temperate Japonica | 767 | 29.30% | 59.30% | 7.95% | 3.39% | NA |
| Tropical Japonica | 504 | 38.10% | 1.60% | 5.75% | 54.56% | NA |
| Japonica Intermediate | 241 | 60.20% | 15.40% | 8.30% | 16.18% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 3.12% | 2.08% | NA |
| Intermediate | 90 | 31.10% | 7.80% | 30.00% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0216594509 | A -> G | LOC_Os02g28020.1 | missense_variant ; p.Phe238Ser; MODERATE | nonsynonymous_codon ; F238P | Average:42.393; most accessible tissue: Minghui63 young leaf, score: 71.254 | unknown | unknown | DELETERIOUS | 0.02 |
| vg0216594509 | A -> G | LOC_Os02g28020.1 | missense_variant ; p.Phe238Ser; MODERATE | nonsynonymous_codon ; F238S | Average:42.393; most accessible tissue: Minghui63 young leaf, score: 71.254 | unknown | unknown | TOLERATED | 0.24 |
| vg0216594509 | A -> DEL | LOC_Os02g28020.1 | N | frameshift_variant | Average:42.393; most accessible tissue: Minghui63 young leaf, score: 71.254 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0216594509 | NA | 8.08E-15 | Grain_length | 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 |
| vg0216594509 | NA | 2.94E-06 | mr1401 | Jap_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 |
| vg0216594509 | NA | 9.22E-07 | mr1627_2 | Jap_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 |
| vg0216594509 | NA | 1.77E-07 | mr1748_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 |