| Variant ID: vg0410291056 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10291056 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 254. )
AAATTCCCGCGTTATCACTGTTTTATCTAGCCATGCCTATTTACCTTTGTTATGACCTTATTATTGTTATTGTATTATTTCCTTGTTCACCCTAGAATAA[A/G]
CAAAACCCCAACTAGTGGACACTCTACTCATGGTACCACTAGTATGATTTTAGGTAGATGCTTCGCTGGTTAATTAGGCAACATTAGGTGGTTTTACAAC
GTTGTAAAACCACCTAATGTTGCCTAATTAACCAGCGAAGCATCTACCTAAAATCATACTAGTGGTACCATGAGTAGAGTGTCCACTAGTTGGGGTTTTG[T/C]
TTATTCTAGGGTGAACAAGGAAATAATACAATAACAATAATAAGGTCATAACAAAGGTAAATAGGCATGGCTAGATAAAACAGTGATAACGCGGGAATTT
| 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 | 23.90% | 0.60% | 44.46% | 31.08% | NA |
| All Indica | 2759 | 6.10% | 0.70% | 68.00% | 25.30% | NA |
| All Japonica | 1512 | 62.00% | 0.50% | 0.66% | 36.84% | NA |
| Aus | 269 | 1.10% | 0.00% | 66.54% | 32.34% | NA |
| Indica I | 595 | 8.70% | 0.70% | 44.03% | 46.55% | NA |
| Indica II | 465 | 7.70% | 1.30% | 62.80% | 28.17% | NA |
| Indica III | 913 | 2.20% | 0.00% | 87.84% | 9.97% | NA |
| Indica Intermediate | 786 | 7.50% | 1.00% | 66.16% | 25.32% | NA |
| Temperate Japonica | 767 | 96.10% | 0.00% | 0.13% | 3.78% | NA |
| Tropical Japonica | 504 | 6.70% | 1.60% | 0.99% | 90.67% | NA |
| Japonica Intermediate | 241 | 68.90% | 0.00% | 1.66% | 29.46% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 6.25% | 93.75% | NA |
| Intermediate | 90 | 25.60% | 0.00% | 33.33% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410291056 | A -> DEL | N | N | silent_mutation | Average:9.242; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0410291056 | A -> G | LOC_Os04g18610.1 | upstream_gene_variant ; 363.0bp to feature; MODIFIER | silent_mutation | Average:9.242; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0410291056 | A -> G | LOC_Os04g18620.1 | downstream_gene_variant ; 4978.0bp to feature; MODIFIER | silent_mutation | Average:9.242; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0410291056 | A -> G | LOC_Os04g18600-LOC_Os04g18610 | intergenic_region ; MODIFIER | silent_mutation | Average:9.242; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0410291056 | NA | 1.68E-08 | mr1217 | 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 |
| vg0410291056 | 9.42E-08 | 8.04E-10 | mr1439 | 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 |
| vg0410291056 | NA | 3.75E-06 | mr1439 | 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 |
| vg0410291056 | NA | 2.00E-08 | mr1845 | 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 |
| vg0410291056 | NA | 4.09E-07 | mr1852 | 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 |