| Variant ID: vg0217093461 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 17093461 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, A: 0.16, others allele: 0.00, population size: 86. )
TGGACTCTAGTCTGCTCTTCTAATATTCTTTATTTTTTAATTCCGAATTTCAGCTATTTATAAATCTTTTTCTTTTCTCCAATTAATGTGAGAATTTTAG[G/A]
TCATGAGAGCGAACGTGGAGGCTCCTTTTTATTCCGAATTTTAGTTAGTTTTAAATTCTTATATGGACCCTATACTCTACTTCTAATATTCCTTATTTTT
AAAAATAAGGAATATTAGAAGTAGAGTATAGGGTCCATATAAGAATTTAAAACTAACTAAAATTCGGAATAAAAAGGAGCCTCCACGTTCGCTCTCATGA[C/T]
CTAAAATTCTCACATTAATTGGAGAAAAGAAAAAGATTTATAAATAGCTGAAATTCGGAATTAAAAAATAAAGAATATTAGAAGAGCAGACTAGAGTCCA
| 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 | 85.10% | 14.30% | 0.61% | 0.00% | NA |
| All Indica | 2759 | 81.60% | 17.80% | 0.69% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 33.10% | 63.60% | 3.35% | 0.00% | NA |
| Indica I | 595 | 77.50% | 21.80% | 0.67% | 0.00% | NA |
| Indica II | 465 | 72.90% | 26.50% | 0.65% | 0.00% | NA |
| Indica III | 913 | 87.50% | 11.80% | 0.66% | 0.00% | NA |
| Indica Intermediate | 786 | 82.80% | 16.40% | 0.76% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 8.90% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0217093461 | G -> A | LOC_Os02g28870.1 | downstream_gene_variant ; 4535.0bp to feature; MODIFIER | silent_mutation | Average:31.591; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg0217093461 | G -> A | LOC_Os02g28880.1 | downstream_gene_variant ; 1112.0bp to feature; MODIFIER | silent_mutation | Average:31.591; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg0217093461 | G -> A | LOC_Os02g28880-LOC_Os02g28890 | intergenic_region ; MODIFIER | silent_mutation | Average:31.591; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0217093461 | NA | 4.93E-10 | mr1109 | Ind_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 |
| vg0217093461 | NA | 8.72E-11 | mr1129 | Ind_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 |
| vg0217093461 | NA | 2.79E-06 | mr1251 | Ind_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 |
| vg0217093461 | NA | 1.13E-06 | mr1253 | Ind_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 |
| vg0217093461 | NA | 1.48E-07 | mr1255 | Ind_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 |
| vg0217093461 | NA | 3.16E-06 | mr1257 | Ind_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 |
| vg0217093461 | 3.57E-25 | 9.67E-42 | mr1317 | 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 |
| vg0217093461 | 6.32E-23 | 1.59E-40 | mr1317 | Ind_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 |
| vg0217093461 | 2.05E-07 | 4.37E-10 | mr1350 | Ind_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 |
| vg0217093461 | NA | 1.63E-06 | mr1409 | Ind_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 |
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