| Variant ID: vg0123793333 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 23793333 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 97. )
CGGTGGAGGCTTATGCAAAGTCCTTCGACACACCACTTCCGTTGCATGTCATCGCCGGTCTGCGGGTGCTCACACGCCTGGATGGAGTGCACGACATGCC[G/A]
GTGCCAGGAGAGGAAGGAACCACCACAACGGCGGTGGTCTGAGGCACGCGCTGCCGCGCCCTGAGAGAAGTCGTCAGCTGTCATGATTGTCCGCATCAGT
ACTGATGCGGACAATCATGACAGCTGACGACTTCTCTCAGGGCGCGGCAGCGCGTGCCTCAGACCACCGCCGTTGTGGTGGTTCCTTCCTCTCCTGGCAC[C/T]
GGCATGTCGTGCACTCCATCCAGGCGTGTGAGCACCCGCAGACCGGCGATGACATGCAACGGAAGTGGTGTGTCGAAGGACTTTGCATAAGCCTCCACCG
| 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 | 52.50% | 4.20% | 9.69% | 33.69% | NA |
| All Indica | 2759 | 45.20% | 0.40% | 8.81% | 45.56% | NA |
| All Japonica | 1512 | 75.70% | 6.50% | 2.25% | 15.54% | NA |
| Aus | 269 | 5.90% | 0.00% | 65.80% | 28.25% | NA |
| Indica I | 595 | 31.60% | 0.00% | 1.34% | 67.06% | NA |
| Indica II | 465 | 84.30% | 0.60% | 0.86% | 14.19% | NA |
| Indica III | 913 | 29.80% | 0.20% | 16.21% | 53.78% | NA |
| Indica Intermediate | 786 | 50.40% | 0.80% | 10.56% | 38.30% | NA |
| Temperate Japonica | 767 | 98.70% | 0.30% | 0.26% | 0.78% | NA |
| Tropical Japonica | 504 | 46.40% | 13.30% | 3.97% | 36.31% | NA |
| Japonica Intermediate | 241 | 63.90% | 12.00% | 4.98% | 19.09% | NA |
| VI/Aromatic | 96 | 9.40% | 83.30% | 1.04% | 6.25% | NA |
| Intermediate | 90 | 67.80% | 8.90% | 3.33% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0123793333 | G -> A | LOC_Os01g41960.1 | synonymous_variant ; p.Pro1202Pro; LOW | synonymous_codon | Average:46.724; most accessible tissue: Zhenshan97 flower, score: 63.813 | N | N | N | N |
| vg0123793333 | G -> DEL | LOC_Os01g41960.1 | N | frameshift_variant | Average:46.724; most accessible tissue: Zhenshan97 flower, score: 63.813 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0123793333 | NA | 4.85E-06 | mr1448 | 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 |
| vg0123793333 | 3.37E-08 | 3.37E-08 | mr1994 | 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 |