| Variant ID: vg1223974671 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 23974671 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.86, T: 0.14, others allele: 0.00, population size: 92. )
TACCTCGATCCGATCGCGCACGCCTCTCCGATCTCCGCGCCGATCTTTTTTCTCGGTTGGTGTTACCAACCGGGACTACAAATAGATCTTTGTTACCAAC[T/C]
GGTACTAAAGATTGAAAAGTACCCTGGAGCTTTTAAACCGGGACTAAAGATGTTTTTAGTCCTGGTTTTTAATACAGCTGGGACTATTATGAAATCTGGT
ACCAGATTTCATAATAGTCCCAGCTGTATTAAAAACCAGGACTAAAAACATCTTTAGTCCCGGTTTAAAAGCTCCAGGGTACTTTTCAATCTTTAGTACC[A/G]
GTTGGTAACAAAGATCTATTTGTAGTCCCGGTTGGTAACACCAACCGAGAAAAAAGATCGGCGCGGAGATCGGAGAGGCGTGCGCGATCGGATCGAGGTA
| 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 | 76.70% | 20.60% | 2.64% | 0.00% | NA |
| All Indica | 2759 | 67.50% | 28.40% | 4.13% | 0.00% | NA |
| All Japonica | 1512 | 87.80% | 11.80% | 0.33% | 0.00% | NA |
| Aus | 269 | 98.10% | 0.00% | 1.86% | 0.00% | NA |
| Indica I | 595 | 50.30% | 41.20% | 8.57% | 0.00% | NA |
| Indica II | 465 | 58.50% | 34.60% | 6.88% | 0.00% | NA |
| Indica III | 913 | 76.80% | 23.10% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 74.90% | 21.20% | 3.82% | 0.00% | NA |
| Temperate Japonica | 767 | 89.20% | 10.20% | 0.65% | 0.00% | NA |
| Tropical Japonica | 504 | 94.00% | 6.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 70.50% | 29.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 11.10% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1223974671 | T -> C | LOC_Os12g38980.1 | upstream_gene_variant ; 3019.0bp to feature; MODIFIER | silent_mutation | Average:29.921; most accessible tissue: Zhenshan97 young leaf, score: 51.997 | N | N | N | N |
| vg1223974671 | T -> C | LOC_Os12g38980-LOC_Os12g38990 | intergenic_region ; MODIFIER | silent_mutation | Average:29.921; most accessible tissue: Zhenshan97 young leaf, score: 51.997 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1223974671 | 3.14E-06 | 3.14E-06 | mr1038 | 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 |
| vg1223974671 | NA | 3.52E-06 | mr1123 | 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 |
| vg1223974671 | NA | 4.90E-06 | mr1745 | 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 |