| Variant ID: vg0412455940 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 12455940 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 96. )
ACCACGCCCGGCAAGTCGACGACGGCACCCGTGTGCATTCAACTTGCGCCCAGGAACCCACCTCCGCCTGCAGCTCCCGCAGCTCCTCCAGTTCTGCCCC[A/G]
CAGTTGCCGCAGCTCCTGCAGCTCCAGAGCCAGTCCCAGCTCATGTTCCAGTGTCAGCTCCCGTGTCCGCTCTCTCCTTCGCTCCAGCATCAGCCGTCAG
CTGACGGCTGATGCTGGAGCGAAGGAGAGAGCGGACACGGGAGCTGACACTGGAACATGAGCTGGGACTGGCTCTGGAGCTGCAGGAGCTGCGGCAACTG[T/C]
GGGGCAGAACTGGAGGAGCTGCGGGAGCTGCAGGCGGAGGTGGGTTCCTGGGCGCAAGTTGAATGCACACGGGTGCCGTCGTCGACTTGCCGGGCGTGGT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.00% | 5.80% | 15.95% | 40.25% | NA |
| All Indica | 2759 | 5.80% | 9.80% | 24.94% | 59.48% | NA |
| All Japonica | 1512 | 99.10% | 0.10% | 0.33% | 0.53% | NA |
| Aus | 269 | 1.10% | 0.40% | 17.10% | 81.41% | NA |
| Indica I | 595 | 6.60% | 5.40% | 14.79% | 73.28% | NA |
| Indica II | 465 | 8.60% | 14.80% | 33.12% | 43.44% | NA |
| Indica III | 913 | 4.20% | 7.80% | 27.16% | 60.90% | NA |
| Indica Intermediate | 786 | 5.50% | 12.50% | 25.19% | 56.87% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.26% | 0.13% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.20% | 0.99% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.40% | 0.83% | 0.83% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 5.21% | 6.25% | NA |
| Intermediate | 90 | 54.40% | 3.30% | 11.11% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0412455940 | A -> DEL | LOC_Os04g22000.1 | N | frameshift_variant | Average:31.649; most accessible tissue: Zhenshan97 root, score: 44.635 | N | N | N | N |
| vg0412455940 | A -> G | LOC_Os04g22000.1 | missense_variant ; p.His222Arg; MODERATE | nonsynonymous_codon ; H222R | Average:31.649; most accessible tissue: Zhenshan97 root, score: 44.635 | unknown | unknown | TOLERATED | 0.87 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0412455940 | 3.27E-07 | NA | mr1071_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 |
| vg0412455940 | 2.60E-07 | NA | mr1080_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 |
| vg0412455940 | 9.90E-08 | NA | mr1203_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 |
| vg0412455940 | 9.65E-06 | NA | mr1613_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 |