| Variant ID: vg0726455031 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 26455031 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTTTTGCACCTCCTTCCAGCGGAGTGGAGGTAGGTATGACCCATCCCATCGGAGGGTCATTCGAACAGCAGCCATTGCAAATCTCCGCCCATTTATGAAG[G/A]
GATGACAGGGTGATCTCCGAGGTTAGACGAGCGAGGACGCCTGGCCACACTCAAGAACAAGCTGTGTTTTAGCTTCCAAGAGAAGGCGAGCCAAGTTTTG
CAAAACTTGGCTCGCCTTCTCTTGGAAGCTAAAACACAGCTTGTTCTTGAGTGTGGCCAGGCGTCCTCGCTCGTCTAACCTCGGAGATCACCCTGTCATC[C/T]
CTTCATAAATGGGCGGAGATTTGCAATGGCTGCTGTTCGAATGACCCTCCGATGGGATGGGTCATACCTACCTCCACTCCGCTGGAAGGAGGTGCAAAAC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 80.60% | 1.30% | 1.12% | 17.03% | NA |
| All Indica | 2759 | 88.60% | 0.00% | 1.30% | 10.11% | NA |
| All Japonica | 1512 | 68.10% | 4.00% | 0.73% | 27.18% | NA |
| Aus | 269 | 60.20% | 0.00% | 1.86% | 37.92% | NA |
| Indica I | 595 | 80.20% | 0.00% | 2.02% | 17.82% | NA |
| Indica II | 465 | 94.20% | 0.00% | 2.37% | 3.44% | NA |
| Indica III | 913 | 91.50% | 0.00% | 0.55% | 8.00% | NA |
| Indica Intermediate | 786 | 88.30% | 0.00% | 1.02% | 10.69% | NA |
| Temperate Japonica | 767 | 93.10% | 0.30% | 0.39% | 6.26% | NA |
| Tropical Japonica | 504 | 36.10% | 2.40% | 1.19% | 60.32% | NA |
| Japonica Intermediate | 241 | 55.20% | 19.50% | 0.83% | 24.48% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 0.00% | 0.00% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0726455031 | G -> DEL | N | N | silent_mutation | Average:23.044; most accessible tissue: Callus, score: 40.331 | N | N | N | N |
| vg0726455031 | G -> A | LOC_Os07g44260.1 | upstream_gene_variant ; 4561.0bp to feature; MODIFIER | silent_mutation | Average:23.044; most accessible tissue: Callus, score: 40.331 | N | N | N | N |
| vg0726455031 | G -> A | LOC_Os07g44280.1 | downstream_gene_variant ; 1690.0bp to feature; MODIFIER | silent_mutation | Average:23.044; most accessible tissue: Callus, score: 40.331 | N | N | N | N |
| vg0726455031 | G -> A | LOC_Os07g44260-LOC_Os07g44280 | intergenic_region ; MODIFIER | silent_mutation | Average:23.044; most accessible tissue: Callus, score: 40.331 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0726455031 | NA | 3.02E-06 | mr1082 | 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 |
| vg0726455031 | 4.09E-06 | 4.09E-06 | mr1436 | 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 |
| vg0726455031 | NA | 3.20E-07 | mr1560 | 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 |
| vg0726455031 | NA | 8.21E-06 | mr1861_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 |