| Variant ID: vg0103230699 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 3230699 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 92. )
ATGAGTATCTAGAGATCGCCCAAACCTCGTAGACTGTGACTAGCAGTCGAACTCATATAGGTGTGTTCCTTCTGAGATGTTCTGCAGGTCAACATCTCTG[C/T]
TTGGAGAAGCCACTCGGAACACATTAAGGCATGAGCCATCCTACCATGCAGGAAAGAAGAGAAGCACATCATGGAAATGAGCCCTTTTCAAGGGTCTCTT
AAGAGACCCTTGAAAAGGGCTCATTTCCATGATGTGCTTCTCTTCTTTCCTGCATGGTAGGATGGCTCATGCCTTAATGTGTTCCGAGTGGCTTCTCCAA[G/A]
CAGAGATGTTGACCTGCAGAACATCTCAGAAGGAACACACCTATATGAGTTCGACTGCTAGTCACAGTCTACGAGGTTTGGGCGATCTCTAGATACTCAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.40% | 1.40% | 19.53% | 47.67% | NA |
| All Indica | 2759 | 32.70% | 2.10% | 30.26% | 34.94% | NA |
| All Japonica | 1512 | 17.10% | 0.40% | 3.97% | 78.51% | NA |
| Aus | 269 | 90.30% | 0.00% | 5.58% | 4.09% | NA |
| Indica I | 595 | 24.20% | 3.00% | 37.82% | 34.96% | NA |
| Indica II | 465 | 35.70% | 4.10% | 29.25% | 30.97% | NA |
| Indica III | 913 | 37.20% | 1.00% | 26.94% | 34.83% | NA |
| Indica Intermediate | 786 | 32.10% | 1.50% | 29.01% | 37.40% | NA |
| Temperate Japonica | 767 | 22.40% | 0.00% | 1.30% | 76.27% | NA |
| Tropical Japonica | 504 | 6.20% | 1.20% | 8.33% | 84.33% | NA |
| Japonica Intermediate | 241 | 23.20% | 0.00% | 3.32% | 73.44% | NA |
| VI/Aromatic | 96 | 53.10% | 0.00% | 1.04% | 45.83% | NA |
| Intermediate | 90 | 34.40% | 0.00% | 13.33% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0103230699 | C -> T | LOC_Os01g06800.1 | upstream_gene_variant ; 917.0bp to feature; MODIFIER | silent_mutation | Average:11.284; most accessible tissue: Minghui63 young leaf, score: 15.967 | N | N | N | N |
| vg0103230699 | C -> T | LOC_Os01g06790.1 | downstream_gene_variant ; 4442.0bp to feature; MODIFIER | silent_mutation | Average:11.284; most accessible tissue: Minghui63 young leaf, score: 15.967 | N | N | N | N |
| vg0103230699 | C -> T | LOC_Os01g06810.1 | downstream_gene_variant ; 186.0bp to feature; MODIFIER | silent_mutation | Average:11.284; most accessible tissue: Minghui63 young leaf, score: 15.967 | N | N | N | N |
| vg0103230699 | C -> T | LOC_Os01g06800-LOC_Os01g06810 | intergenic_region ; MODIFIER | silent_mutation | Average:11.284; most accessible tissue: Minghui63 young leaf, score: 15.967 | N | N | N | N |
| vg0103230699 | C -> DEL | N | N | silent_mutation | Average:11.284; most accessible tissue: Minghui63 young leaf, score: 15.967 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0103230699 | 9.08E-06 | NA | mr1328 | 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 |
| vg0103230699 | 7.10E-07 | 7.10E-07 | mr1967 | 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 |
| vg0103230699 | 2.76E-06 | 8.70E-07 | mr1027_2 | Jap_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 |