| Variant ID: vg0912516801 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 12516801 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.24, others allele: 0.00, population size: 89. )
ATGGACCGAGTAACGCAAGGTGCTAAGTATTATTTGGAATAAATCAAAAGCATAGAGATAAGATAAATTTATTTTCTGCTCTTTACAATTGCAAAAGTAC[T/C]
CAAGTAGTAAATTCTGATTCGTGAAGTTTTGTTCCATTAATGACGAACTTATGTCACTCATATGCATGTTTGGGAAGTGCCTAGGCCGACTCCCGATGCT
AGCATCGGGAGTCGGCCTAGGCACTTCCCAAACATGCATATGAGTGACATAAGTTCGTCATTAATGGAACAAAACTTCACGAATCAGAATTTACTACTTG[A/G]
GTACTTTTGCAATTGTAAAGAGCAGAAAATAAATTTATCTTATCTCTATGCTTTTGATTTATTCCAAATAATACTTAGCACCTTGCGTTACTCGGTCCAT
| 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 | 37.90% | 18.50% | 3.34% | 40.18% | NA |
| All Indica | 2759 | 4.90% | 29.00% | 5.44% | 60.71% | NA |
| All Japonica | 1512 | 94.20% | 0.50% | 0.13% | 5.09% | NA |
| Aus | 269 | 40.10% | 13.40% | 0.37% | 46.10% | NA |
| Indica I | 595 | 8.90% | 9.40% | 0.34% | 81.34% | NA |
| Indica II | 465 | 4.30% | 16.80% | 13.76% | 65.16% | NA |
| Indica III | 913 | 0.70% | 51.20% | 4.71% | 43.48% | NA |
| Indica Intermediate | 786 | 7.10% | 25.20% | 5.22% | 62.47% | NA |
| Temperate Japonica | 767 | 97.80% | 0.40% | 0.13% | 1.69% | NA |
| Tropical Japonica | 504 | 88.10% | 1.00% | 0.00% | 10.91% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 0.41% | 3.73% | NA |
| VI/Aromatic | 96 | 70.80% | 19.80% | 1.04% | 8.33% | NA |
| Intermediate | 90 | 63.30% | 15.60% | 4.44% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0912516801 | T -> DEL | N | N | silent_mutation | Average:13.058; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0912516801 | T -> C | LOC_Os09g20780.1 | upstream_gene_variant ; 4156.0bp to feature; MODIFIER | silent_mutation | Average:13.058; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0912516801 | T -> C | LOC_Os09g20790.1 | downstream_gene_variant ; 4961.0bp to feature; MODIFIER | silent_mutation | Average:13.058; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0912516801 | T -> C | LOC_Os09g20770.1 | intron_variant ; MODIFIER | silent_mutation | Average:13.058; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0912516801 | NA | 6.77E-07 | mr1352 | 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 |
| vg0912516801 | NA | 5.26E-07 | mr1215_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 |
| vg0912516801 | NA | 5.78E-08 | mr1242_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 |
| vg0912516801 | NA | 3.37E-07 | mr1422_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 |