| Variant ID: vg1222217188 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22217188 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.09, others allele: 0.00, population size: 177. )
CAGCTCCTCCTATCGGCATCCTACAGCCAAGATGGCGGCCTGCACACACTGCTGCAGTCACTTGATTGTACGAGGGCATACAATGCCGAGGCGAGGGAGC[A/G]
CGCTGCAAGGATCGTGGCGCACCTTGCTGGTGACCTCCACCTGGAGCAGTTTCCACAAGGGATCCATTGCATAGCTTCTCTGCTCGAAGGTCCCCCTAAG
CTTAGGGGGACCTTCGAGCAGAGAAGCTATGCAATGGATCCCTTGTGGAAACTGCTCCAGGTGGAGGTCACCAGCAAGGTGCGCCACGATCCTTGCAGCG[T/C]
GCTCCCTCGCCTCGGCATTGTATGCCCTCGTACAATCAAGTGACTGCAGCAGTGTGTGCAGGCCGCCATCTTGGCTGTAGGATGCCGATAGGAGGAGCTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.80% | 19.40% | 0.70% | 14.09% | NA |
| All Indica | 2759 | 82.60% | 3.80% | 0.72% | 12.83% | NA |
| All Japonica | 1512 | 41.00% | 43.80% | 0.33% | 14.81% | NA |
| Aus | 269 | 21.90% | 46.10% | 2.23% | 29.74% | NA |
| Indica I | 595 | 95.60% | 1.30% | 0.17% | 2.86% | NA |
| Indica II | 465 | 76.80% | 3.20% | 0.65% | 19.35% | NA |
| Indica III | 913 | 77.20% | 5.40% | 0.55% | 16.87% | NA |
| Indica Intermediate | 786 | 82.60% | 4.20% | 1.40% | 11.83% | NA |
| Temperate Japonica | 767 | 16.90% | 72.10% | 0.26% | 10.69% | NA |
| Tropical Japonica | 504 | 67.50% | 11.90% | 0.40% | 20.24% | NA |
| Japonica Intermediate | 241 | 62.20% | 20.70% | 0.41% | 16.60% | NA |
| VI/Aromatic | 96 | 93.80% | 2.10% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 70.00% | 23.30% | 2.22% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222217188 | A -> DEL | LOC_Os12g36270.1 | N | frameshift_variant | Average:71.415; most accessible tissue: Zhenshan97 young leaf, score: 87.859 | N | N | N | N |
| vg1222217188 | A -> G | LOC_Os12g36270.1 | missense_variant ; p.His338Arg; MODERATE | nonsynonymous_codon ; H338R | Average:71.415; most accessible tissue: Zhenshan97 young leaf, score: 87.859 | unknown | unknown | TOLERATED | 0.35 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1222217188 | NA | 1.22E-06 | mr1330 | 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 |
| vg1222217188 | NA | 5.70E-08 | mr1763 | 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 |
| vg1222217188 | 5.32E-06 | NA | mr1805_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 |