| Variant ID: vg0123689616 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 23689616 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, C: 0.08, others allele: 0.00, population size: 109. )
GTGGGTGCGTTCGTTCCAGTGACATTGGGTGAGAAAACACCTCGTTTTTCGTGTGTACACTTCCCAAACTACTAAACGGTGTGGCTTTTTGTAAAAAATT[T/C]
CTGTAGGAAAGTTACTTTAAAAAATTTTGTAAAAAATTTCTATAGGAAAGTTGCTTTAAAAAATCATATTAATCTATTTTTGCATTTTAAAATAGTTAAT
ATTAACTATTTTAAAATGCAAAAATAGATTAATATGATTTTTTAAAGCAACTTTCCTATAGAAATTTTTTACAAAATTTTTTAAAGTAACTTTCCTACAG[A/G]
AATTTTTTACAAAAAGCCACACCGTTTAGTAGTTTGGGAAGTGTACACACGAAAAACGAGGTGTTTTCTCACCCAATGTCACTGGAACGAACGCACCCAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.80% | 44.90% | 0.04% | 0.25% | NA |
| All Indica | 2759 | 48.90% | 50.70% | 0.04% | 0.43% | NA |
| All Japonica | 1512 | 77.20% | 22.80% | 0.07% | 0.00% | NA |
| Aus | 269 | 9.30% | 90.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 60.30% | 39.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 15.50% | 84.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 65.80% | 33.40% | 0.00% | 0.77% | NA |
| Indica Intermediate | 786 | 40.20% | 59.00% | 0.13% | 0.64% | NA |
| Temperate Japonica | 767 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 51.20% | 48.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 61.40% | 38.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 7.30% | 92.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 48.90% | 51.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0123689616 | T -> DEL | N | N | silent_mutation | Average:86.475; most accessible tissue: Zhenshan97 root, score: 94.124 | N | N | N | N |
| vg0123689616 | T -> C | LOC_Os01g41820.1 | upstream_gene_variant ; 4223.0bp to feature; MODIFIER | silent_mutation | Average:86.475; most accessible tissue: Zhenshan97 root, score: 94.124 | N | N | N | N |
| vg0123689616 | T -> C | LOC_Os01g41834.1 | intron_variant ; MODIFIER | silent_mutation | Average:86.475; most accessible tissue: Zhenshan97 root, score: 94.124 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0123689616 | NA | 1.28E-08 | mr1593 | 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 |
| vg0123689616 | 2.04E-07 | NA | mr1079_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 |
| vg0123689616 | NA | 2.39E-11 | mr1593_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 |
| vg0123689616 | NA | 1.50E-07 | mr1808_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 |