| Variant ID: vg0314575940 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 14575940 |
| 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: 259. )
AAGGGTATTGTCACGATTTCCCCCTTTGCAATGCCGTGGTGGTATTACGGGGCATGGCAACATGTGTGGAATCGTGTCTTGTGGGTACAGTGGTACACCT[C/T]
TGGCTAGAGTAAAACTATTCGAATAGCCGTGCCCGCGGTCATGGGCGAGTTGAGCAATGTTTTTCGTGATTAGTCCCATACTACTCAATAATGTTAATAA
TTATTAACATTATTGAGTAGTATGGGACTAATCACGAAAAACATTGCTCAACTCGCCCATGACCGCGGGCACGGCTATTCGAATAGTTTTACTCTAGCCA[G/A]
AGGTGTACCACTGTACCCACAAGACACGATTCCACACATGTTGCCATGCCCCGTAATACCACCACGGCATTGCAAAGGGGGAAATCGTGACAATACCCTT
| 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 | 96.10% | 1.80% | 2.09% | 0.00% | NA |
| All Indica | 2759 | 93.90% | 2.80% | 3.33% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 97.00% | 2.20% | 0.74% | 0.00% | NA |
| Indica I | 595 | 91.40% | 3.40% | 5.21% | 0.00% | NA |
| Indica II | 465 | 84.90% | 6.70% | 8.39% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.40% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 94.80% | 2.80% | 2.42% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 1.10% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0314575940 | C -> T | LOC_Os03g25510.1 | upstream_gene_variant ; 1165.0bp to feature; MODIFIER | silent_mutation | Average:55.982; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg0314575940 | C -> T | LOC_Os03g25530.1 | upstream_gene_variant ; 2599.0bp to feature; MODIFIER | silent_mutation | Average:55.982; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg0314575940 | C -> T | LOC_Os03g25500.1 | downstream_gene_variant ; 4177.0bp to feature; MODIFIER | silent_mutation | Average:55.982; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| vg0314575940 | C -> T | LOC_Os03g25510-LOC_Os03g25530 | intergenic_region ; MODIFIER | silent_mutation | Average:55.982; most accessible tissue: Minghui63 flag leaf, score: 76.091 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0314575940 | 2.46E-06 | NA | mr1542 | 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 |
| vg0314575940 | NA | 1.47E-12 | mr1542 | 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 |
| vg0314575940 | NA | 1.97E-12 | mr1542_2 | 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 |