| Variant ID: vg0718406689 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 18406689 |
| 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: 112. )
CTCAGCGGACACCATGTGAGCTGCATATCCCCTTCAAGAACTTATCAATAAAGGTAAACTCGTAGTTTATAGATTTTAGATTTGGCCATTCCGCTAGTTG[C/T]
TGCTTATATATGTTGATTACTAATAAATAACCTCTCACCACATGAAGGTGGCGTCGGGCATGGCCATCTCAACGGACCCTTCAGGTACTTACCACTACAG
CTGTAGTGGTAAGTACCTGAAGGGTCCGTTGAGATGGCCATGCCCGACGCCACCTTCATGTGGTGAGAGGTTATTTATTAGTAATCAACATATATAAGCA[G/A]
CAACTAGCGGAATGGCCAAATCTAAAATCTATAAACTACGAGTTTACCTTTATTGATAAGTTCTTGAAGGGGATATGCAGCTCACATGGTGTCCGCTGAG
| 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 | 70.90% | 24.90% | 1.16% | 3.00% | NA |
| All Indica | 2759 | 77.10% | 22.10% | 0.62% | 0.11% | NA |
| All Japonica | 1512 | 58.90% | 29.80% | 2.25% | 9.06% | NA |
| Aus | 269 | 98.50% | 0.40% | 1.12% | 0.00% | NA |
| Indica I | 595 | 82.40% | 17.00% | 0.50% | 0.17% | NA |
| Indica II | 465 | 89.70% | 10.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 72.50% | 26.30% | 0.99% | 0.22% | NA |
| Indica Intermediate | 786 | 71.10% | 28.20% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 76.40% | 21.30% | 0.52% | 1.83% | NA |
| Tropical Japonica | 504 | 39.50% | 38.70% | 4.76% | 17.06% | NA |
| Japonica Intermediate | 241 | 43.60% | 38.60% | 2.49% | 15.35% | NA |
| VI/Aromatic | 96 | 11.50% | 87.50% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 65.60% | 32.20% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0718406689 | C -> DEL | N | N | silent_mutation | Average:25.079; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |
| vg0718406689 | C -> T | LOC_Os07g31110.1 | upstream_gene_variant ; 1248.0bp to feature; MODIFIER | silent_mutation | Average:25.079; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |
| vg0718406689 | C -> T | LOC_Os07g31080.1 | downstream_gene_variant ; 3301.0bp to feature; MODIFIER | silent_mutation | Average:25.079; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |
| vg0718406689 | C -> T | LOC_Os07g31090.1 | downstream_gene_variant ; 1108.0bp to feature; MODIFIER | silent_mutation | Average:25.079; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |
| vg0718406689 | C -> T | LOC_Os07g31100.1 | intron_variant ; MODIFIER | silent_mutation | Average:25.079; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0718406689 | NA | 3.99E-07 | mr1167_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 |
| vg0718406689 | NA | 1.44E-06 | mr1479_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 |
| vg0718406689 | NA | 4.54E-06 | mr1502_2 | Ind_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 |
| vg0718406689 | NA | 5.28E-06 | mr1950_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 |