| Variant ID: vg0910099182 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10099182 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.02, others allele: 0.00, population size: 200. )
AAGTGATCTTAGACCCATTAGGGGGATGAATTAATTATCATGTTTGCCATGGTTAGGAAGATCAAAGTTGCTACTGTGAAATGTATGATAAGGCAATGGT[T/C]
AGAAAGTATAAGATTTTCTGCTCCTGTTGAGTGCAGTTCTTTGATTACTCGGATAGCCAAGGGACTAGGGGACGTCAATGACCAGATTGCTTATATCTCA
TGAGATATAAGCAATCTGGTCATTGACGTCCCCTAGTCCCTTGGCTATCCGAGTAATCAAAGAACTGCACTCAACAGGAGCAGAAAATCTTATACTTTCT[A/G]
ACCATTGCCTTATCATACATTTCACAGTAGCAACTTTGATCTTCCTAACCATGGCAAACATGATAATTAATTCATCCCCCTAATGGGTCTAAGATCACTT
| 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 | 58.80% | 34.70% | 3.98% | 2.58% | NA |
| All Indica | 2759 | 33.80% | 57.60% | 4.53% | 4.10% | NA |
| All Japonica | 1512 | 95.60% | 0.50% | 3.57% | 0.33% | NA |
| Aus | 269 | 91.40% | 7.10% | 1.12% | 0.37% | NA |
| Indica I | 595 | 18.30% | 71.30% | 6.89% | 3.53% | NA |
| Indica II | 465 | 35.30% | 58.10% | 3.87% | 2.80% | NA |
| Indica III | 913 | 39.90% | 51.70% | 3.18% | 5.26% | NA |
| Indica Intermediate | 786 | 37.70% | 53.70% | 4.71% | 3.94% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 89.70% | 0.40% | 9.52% | 0.40% | NA |
| Japonica Intermediate | 241 | 95.00% | 1.20% | 2.49% | 1.24% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 66.70% | 23.30% | 6.67% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910099182 | T -> DEL | N | N | silent_mutation | Average:36.257; most accessible tissue: Zhenshan97 young leaf, score: 57.78 | N | N | N | N |
| vg0910099182 | T -> C | LOC_Os09g16480.1 | downstream_gene_variant ; 1755.0bp to feature; MODIFIER | silent_mutation | Average:36.257; most accessible tissue: Zhenshan97 young leaf, score: 57.78 | N | N | N | N |
| vg0910099182 | T -> C | LOC_Os09g16490.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.257; most accessible tissue: Zhenshan97 young leaf, score: 57.78 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0910099182 | NA | 6.29E-06 | mr1304 | 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 |
| vg0910099182 | NA | 2.29E-06 | mr1401 | 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 |
| vg0910099182 | NA | 5.31E-06 | mr1255_2 | 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 |
| vg0910099182 | NA | 1.19E-08 | mr1498_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 |
| vg0910099182 | 1.07E-06 | NA | mr1539_2 | 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 |
| vg0910099182 | NA | 2.10E-08 | mr1925_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 |