| Variant ID: vg1217370443 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 17370443 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 254. )
TTCAAGGGTCTCTTCTCTCAGTCACACAATAGTTTGTTTCGCCATCCAAATTCACAAGATCTCCGATCACAATGGACAGGTTTCCACTATTGTGCAACCT[T/A]
AGGTGGGTATCAAGCCCATTTCCCTCGATGCACTATCTATCACATTACGTGGTAGCCCCTTGGTAAACTGATCTGCCAGATTTCTAGCCGTTTGGACATA
TATGTCCAAACGGCTAGAAATCTGGCAGATCAGTTTACCAAGGGGCTACCACGTAATGTGATAGATAGTGCATCGAGGGAAATGGGCTTGATACCCACCT[A/T]
AGGTTGCACAATAGTGGAAACCTGTCCATTGTGATCGGAGATCTTGTGAATTTGGATGGCGAAACAAACTATTGTGTGACTGAGAGAAGAGACCCTTGAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.20% | 10.90% | 3.30% | 25.54% | NA |
| All Indica | 2759 | 44.70% | 18.40% | 5.04% | 31.93% | NA |
| All Japonica | 1512 | 89.60% | 0.10% | 0.07% | 10.25% | NA |
| Aus | 269 | 68.40% | 0.40% | 2.97% | 28.25% | NA |
| Indica I | 595 | 63.20% | 23.40% | 1.01% | 12.44% | NA |
| Indica II | 465 | 64.90% | 11.40% | 1.51% | 22.15% | NA |
| Indica III | 913 | 21.90% | 18.10% | 9.97% | 50.05% | NA |
| Indica Intermediate | 786 | 45.00% | 19.10% | 4.45% | 31.42% | NA |
| Temperate Japonica | 767 | 99.50% | 0.10% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 72.80% | 0.20% | 0.20% | 26.79% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.00% | 0.00% | 7.05% | NA |
| VI/Aromatic | 96 | 18.80% | 1.00% | 6.25% | 73.96% | NA |
| Intermediate | 90 | 65.60% | 5.60% | 2.22% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1217370443 | T -> DEL | LOC_Os12g29310.1 | N | frameshift_variant | Average:28.192; most accessible tissue: Zhenshan97 root, score: 55.432 | N | N | N | N |
| vg1217370443 | T -> A | LOC_Os12g29310.1 | stop_lost&splice_region_variant ; p.Ter1200Leuext*?; HIGH | stop_lost | Average:28.192; most accessible tissue: Zhenshan97 root, score: 55.432 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1217370443 | 3.16E-06 | NA | mr1458_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 |
| vg1217370443 | 2.71E-06 | NA | mr1458_2 | 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 |