| Variant ID: vg1125078873 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25078873 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, T: 0.11, others allele: 0.00, population size: 254. )
TGTGCCTATTCTTCCTTCCAATTTGCAAGCAGTACAAAGGCTTTCATCCCTGTCTAGTTGCATGCATGTAACTAACTGCATATATGTGGCCATGGAAATA[G/T]
GTGGCATCCGGGCAAGAGCGATTAGGTGCAAACAGAGCCAGGTTACAGCTGATTCTCCCTCCAAGGATTGGTAAATTAGTATGTGCTCATCTCTGCTCTT
AAGAGCAGAGATGAGCACATACTAATTTACCAATCCTTGGAGGGAGAATCAGCTGTAACCTGGCTCTGTTTGCACCTAATCGCTCTTGCCCGGATGCCAC[C/A]
TATTTCCATGGCCACATATATGCAGTTAGTTACATGCATGCAACTAGACAGGGATGAAAGCCTTTGTACTGCTTGCAAATTGGAAGGAAGAATAGGCACA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.90% | 8.30% | 4.70% | 12.08% | NA |
| All Indica | 2759 | 65.20% | 10.80% | 6.42% | 17.58% | NA |
| All Japonica | 1512 | 97.50% | 0.40% | 0.53% | 1.59% | NA |
| Aus | 269 | 47.60% | 21.20% | 12.64% | 18.59% | NA |
| Indica I | 595 | 60.80% | 15.30% | 4.37% | 19.50% | NA |
| Indica II | 465 | 72.90% | 7.30% | 1.72% | 18.06% | NA |
| Indica III | 913 | 59.10% | 9.60% | 12.16% | 19.06% | NA |
| Indica Intermediate | 786 | 71.00% | 10.80% | 4.07% | 14.12% | NA |
| Temperate Japonica | 767 | 97.30% | 0.30% | 0.39% | 2.09% | NA |
| Tropical Japonica | 504 | 99.40% | 0.20% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.20% | 1.20% | 1.24% | 3.32% | NA |
| VI/Aromatic | 96 | 75.00% | 22.90% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 75.60% | 10.00% | 3.33% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1125078873 | G -> T | LOC_Os11g41760.1 | upstream_gene_variant ; 1847.0bp to feature; MODIFIER | silent_mutation | Average:72.267; most accessible tissue: Zhenshan97 young leaf, score: 83.199 | N | N | N | N |
| vg1125078873 | G -> T | LOC_Os11g41760-LOC_Os11g41770 | intergenic_region ; MODIFIER | silent_mutation | Average:72.267; most accessible tissue: Zhenshan97 young leaf, score: 83.199 | N | N | N | N |
| vg1125078873 | G -> DEL | N | N | silent_mutation | Average:72.267; most accessible tissue: Zhenshan97 young leaf, score: 83.199 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1125078873 | 7.88E-07 | 3.79E-19 | mr1191 | 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 |
| vg1125078873 | 2.92E-06 | 6.35E-12 | mr1191 | 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 |
| vg1125078873 | 1.60E-09 | 9.34E-23 | mr1644 | 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 |
| vg1125078873 | 2.38E-08 | 5.12E-15 | mr1644 | 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 |
| vg1125078873 | 2.84E-09 | 2.93E-33 | mr1191_2 | 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 |
| vg1125078873 | 5.29E-08 | 3.10E-21 | mr1191_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 |