| Variant ID: vg0627981060 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 27981060 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.24, others allele: 0.00, population size: 68. )
CTGCGAATGAAGTTTGTTATTTGTGCGGCTGGTATTATTTTGCCGCGCTTCGCCTCGTGCGATTGATGGTTATATATATTCTTTTTTCCTGGGCCGAACA[A/G]
AACAGTATTGGGCCTTCCTATCTTGGGCTTTTTACTGTGCCGCTCGGTCGATGGGAATTTACCGTTTCGCCTACCCTTGCGACACGTGGCGCTTCATTAC
GTAATGAAGCGCCACGTGTCGCAAGGGTAGGCGAAACGGTAAATTCCCATCGACCGAGCGGCACAGTAAAAAGCCCAAGATAGGAAGGCCCAATACTGTT[T/C]
TGTTCGGCCCAGGAAAAAAGAATATATATAACCATCAATCGCACGAGGCGAAGCGCGGCAAAATAATACCAGCCGCACAAATAACAAACTTCATTCGCAG
| 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 | 49.30% | 30.00% | 9.01% | 11.70% | NA |
| All Indica | 2759 | 35.40% | 44.30% | 9.21% | 11.09% | NA |
| All Japonica | 1512 | 84.90% | 10.60% | 0.33% | 4.17% | NA |
| Aus | 269 | 0.70% | 3.30% | 55.02% | 40.89% | NA |
| Indica I | 595 | 46.60% | 46.10% | 1.68% | 5.71% | NA |
| Indica II | 465 | 54.80% | 41.70% | 2.80% | 0.65% | NA |
| Indica III | 913 | 16.10% | 53.70% | 15.01% | 15.22% | NA |
| Indica Intermediate | 786 | 37.90% | 33.60% | 11.96% | 16.54% | NA |
| Temperate Japonica | 767 | 79.90% | 19.30% | 0.26% | 0.52% | NA |
| Tropical Japonica | 504 | 87.90% | 1.80% | 0.60% | 9.72% | NA |
| Japonica Intermediate | 241 | 94.60% | 1.20% | 0.00% | 4.15% | NA |
| VI/Aromatic | 96 | 17.70% | 3.10% | 11.46% | 67.71% | NA |
| Intermediate | 90 | 55.60% | 25.60% | 8.89% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0627981060 | A -> G | LOC_Os06g46160.1 | upstream_gene_variant ; 1699.0bp to feature; MODIFIER | silent_mutation | Average:53.366; most accessible tissue: Minghui63 flag leaf, score: 66.556 | N | N | N | N |
| vg0627981060 | A -> G | LOC_Os06g46180.1 | downstream_gene_variant ; 4366.0bp to feature; MODIFIER | silent_mutation | Average:53.366; most accessible tissue: Minghui63 flag leaf, score: 66.556 | N | N | N | N |
| vg0627981060 | A -> G | LOC_Os06g46160-LOC_Os06g46180 | intergenic_region ; MODIFIER | silent_mutation | Average:53.366; most accessible tissue: Minghui63 flag leaf, score: 66.556 | N | N | N | N |
| vg0627981060 | A -> DEL | N | N | silent_mutation | Average:53.366; most accessible tissue: Minghui63 flag leaf, score: 66.556 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0627981060 | NA | 8.83E-12 | Awn_length | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0627981060 | NA | 5.59E-08 | mr1462_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 |
| vg0627981060 | NA | 2.23E-08 | mr1582_2 | 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 |
| vg0627981060 | NA | 2.27E-07 | mr1582_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 |