| Variant ID: vg0812028320 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 12028320 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.85, G: 0.16, others allele: 0.00, population size: 145. )
GTGTCCTGAATGCTCCATAGTGACCTCCATATGGGGCAGCATGACACTTCTCAATGATCTTCATGCCTTCATCTACCGGAACGCATCTTCGTAGTAGACC[A/G]
TCTGAACAGACTCTGTACAGGTAAGGTGCATCCCACAAGTGCCTGCGGCTCTCGTAGATCAACCTCTTCTTATTTTCTCCCGTTGGCACACGCCCCGCAA
TTGCGGGGCGTGTGCCAACGGGAGAAAATAAGAAGAGGTTGATCTACGAGAGCCGCAGGCACTTGTGGGATGCACCTTACCTGTACAGAGTCTGTTCAGA[T/C]
GGTCTACTACGAAGATGCGTTCCGGTAGATGAAGGCATGAAGATCATTGAGAAGTGTCATGCTGCCCCATATGGAGGTCACTATGGAGCATTCAGGACAC
| 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 | 65.40% | 9.00% | 17.05% | 8.55% | NA |
| All Indica | 2759 | 50.20% | 9.90% | 26.31% | 13.63% | NA |
| All Japonica | 1512 | 86.70% | 8.50% | 3.24% | 1.52% | NA |
| Aus | 269 | 89.20% | 4.10% | 6.32% | 0.37% | NA |
| Indica I | 595 | 38.70% | 2.70% | 42.86% | 15.80% | NA |
| Indica II | 465 | 49.70% | 6.20% | 25.81% | 18.28% | NA |
| Indica III | 913 | 57.10% | 17.10% | 15.01% | 10.84% | NA |
| Indica Intermediate | 786 | 51.30% | 9.00% | 27.23% | 12.47% | NA |
| Temperate Japonica | 767 | 95.20% | 1.00% | 2.22% | 1.56% | NA |
| Tropical Japonica | 504 | 73.00% | 20.60% | 5.16% | 1.19% | NA |
| Japonica Intermediate | 241 | 88.40% | 7.10% | 2.49% | 2.07% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 72.20% | 7.80% | 15.56% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0812028320 | A -> G | LOC_Os08g20060.1 | synonymous_variant ; p.Asp414Asp; LOW | synonymous_codon | Average:40.12; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0812028320 | A -> G | LOC_Os08g20060.1 | synonymous_variant ; p.Asp414Asp; LOW | nonsynonymous_codon ; D414N | Average:40.12; most accessible tissue: Minghui63 panicle, score: 68.46 | unknown | unknown | TOLERATED | 0.08 |
| vg0812028320 | A -> DEL | LOC_Os08g20060.1 | N | frameshift_variant | Average:40.12; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0812028320 | NA | 8.67E-07 | mr1134 | 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 |
| vg0812028320 | NA | 8.39E-06 | mr1504 | 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 |
| vg0812028320 | NA | 5.90E-06 | mr1695 | 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 |