| Variant ID: vg0401672905 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1672905 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, A: 0.10, others allele: 0.00, population size: 94. )
GGAAAAACCATCACCTCTAAACCCCTCATAGGTAATCCTTGCTTTTTAATTTACCCCTAAACACTTCCTATTATACTTGATATTCTTTTAACTTTTTCCT[T/A]
CAGATTTAATTGGGGTAGTCAGTCGTATTGGTCCATATGATTTCGCGAGCCCAACATCAGACAAAAAACTCAGAAGAATTCAAATTCAGAACCAAGAGTA
TACTCTTGGTTCTGAATTTGAATTCTTCTGAGTTTTTTGTCTGATGTTGGGCTCGCGAAATCATATGGACCAATACGACTGACTACCCCAATTAAATCTG[A/T]
AGGAAAAAGTTAAAAGAATATCAAGTATAATAGGAAGTGTTTAGGGGTAAATTAAAAAGCAAGGATTACCTATGAGGGGTTTAGAGGTGATGGTTTTTCC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 23.80% | 11.60% | 0.40% | 64.13% | NA |
| All Indica | 2759 | 10.90% | 16.60% | 0.58% | 71.91% | NA |
| All Japonica | 1512 | 51.60% | 1.90% | 0.13% | 46.36% | NA |
| Aus | 269 | 8.20% | 4.50% | 0.37% | 86.99% | NA |
| Indica I | 595 | 24.70% | 5.40% | 1.18% | 68.74% | NA |
| Indica II | 465 | 8.20% | 40.40% | 0.22% | 51.18% | NA |
| Indica III | 913 | 1.90% | 6.90% | 0.22% | 91.02% | NA |
| Indica Intermediate | 786 | 12.50% | 22.40% | 0.76% | 64.38% | NA |
| Temperate Japonica | 767 | 82.40% | 0.50% | 0.13% | 16.95% | NA |
| Tropical Japonica | 504 | 16.90% | 3.40% | 0.20% | 79.56% | NA |
| Japonica Intermediate | 241 | 26.10% | 3.30% | 0.00% | 70.54% | NA |
| VI/Aromatic | 96 | 2.10% | 33.30% | 0.00% | 64.58% | NA |
| Intermediate | 90 | 25.60% | 18.90% | 0.00% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401672905 | T -> DEL | N | N | silent_mutation | Average:6.0; most accessible tissue: Callus, score: 21.328 | N | N | N | N |
| vg0401672905 | T -> A | LOC_Os04g03760.1 | downstream_gene_variant ; 3704.0bp to feature; MODIFIER | silent_mutation | Average:6.0; most accessible tissue: Callus, score: 21.328 | N | N | N | N |
| vg0401672905 | T -> A | LOC_Os04g03740-LOC_Os04g03760 | intergenic_region ; MODIFIER | silent_mutation | Average:6.0; most accessible tissue: Callus, score: 21.328 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401672905 | NA | 1.57E-11 | mr1829 | 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 |
| vg0401672905 | 9.13E-07 | NA | mr1842 | 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 |
| vg0401672905 | NA | 3.58E-07 | mr1842 | 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 |
| vg0401672905 | NA | 4.13E-07 | mr1062_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 |
| vg0401672905 | NA | 4.65E-09 | mr1829_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 |