| Variant ID: vg0402921204 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2921204 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 89. )
AACTAACCATCAAGCTACTCATCAATCTAGGTAAGGGGGGGTGTGTCTCGCATACTATCCAAAAACCATCTGAAGCGAGATCGAAACTGCAATAATCCTC[T/C]
AGTCTAGTCATCCGACCATCCGCAGGATCCTGGGGCAGGTAGAAGGTGGTCGCGGGCACGGGCAAACCTGAGTCCCCATGGCTCGGAAGTAGTGGCCTCT
AGAGGCCACTACTTCCGAGCCATGGGGACTCAGGTTTGCCCGTGCCCGCGACCACCTTCTACCTGCCCCAGGATCCTGCGGATGGTCGGATGACTAGACT[A/G]
GAGGATTATTGCAGTTTCGATCTCGCTTCAGATGGTTTTTGGATAGTATGCGAGACACACCCCCCCTTACCTAGATTGATGAGTAGCTTGATGGTTAGTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.50% | 1.60% | 18.62% | 17.22% | NA |
| All Indica | 2759 | 40.20% | 2.50% | 30.41% | 26.89% | NA |
| All Japonica | 1512 | 96.40% | 0.30% | 1.26% | 2.12% | NA |
| Aus | 269 | 89.20% | 0.00% | 3.35% | 7.43% | NA |
| Indica I | 595 | 13.40% | 1.70% | 18.82% | 66.05% | NA |
| Indica II | 465 | 31.20% | 4.90% | 48.17% | 15.70% | NA |
| Indica III | 913 | 56.80% | 2.20% | 28.59% | 12.38% | NA |
| Indica Intermediate | 786 | 46.30% | 2.20% | 30.79% | 20.74% | NA |
| Temperate Japonica | 767 | 94.40% | 0.30% | 1.83% | 3.52% | NA |
| Tropical Japonica | 504 | 98.60% | 0.20% | 0.60% | 0.60% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.40% | 0.83% | 0.83% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 64.40% | 1.10% | 14.44% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402921204 | T -> C | LOC_Os04g05720.1 | upstream_gene_variant ; 687.0bp to feature; MODIFIER | silent_mutation | Average:39.47; most accessible tissue: Minghui63 young leaf, score: 71.254 | N | N | N | N |
| vg0402921204 | T -> C | LOC_Os04g05710.1 | intron_variant ; MODIFIER | silent_mutation | Average:39.47; most accessible tissue: Minghui63 young leaf, score: 71.254 | N | N | N | N |
| vg0402921204 | T -> DEL | N | N | silent_mutation | Average:39.47; most accessible tissue: Minghui63 young leaf, score: 71.254 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402921204 | 1.26E-06 | 3.78E-10 | mr1549 | 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 |
| vg0402921204 | NA | 5.76E-06 | mr1550 | 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 |
| vg0402921204 | 1.96E-07 | 9.24E-11 | mr1757 | 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 |
| vg0402921204 | NA | 2.26E-07 | mr1549_2 | 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 |
| vg0402921204 | NA | 4.21E-07 | mr1757_2 | 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 |