| Variant ID: vg1226733008 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 26733008 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CAGCTTGACCAGGGCTACACCTAATCTTCCACACCATCAGCATCACTGTAGAACTCCTCCTCTGATGAATGATTGCTAGGTGAGTATATGACATACTCAG[C/A]
AAGCCACGCAACAAATATGCAAGTGCACAGGATAACAAAGGATGGCATAGTAGGGTTTCATTTGCATAAACAGCATTTAATAAACATTTCAGAATTTAAT
ATTAAATTCTGAAATGTTTATTAAATGCTGTTTATGCAAATGAAACCCTACTATGCCATCCTTTGTTATCCTGTGCACTTGCATATTTGTTGCGTGGCTT[G/T]
CTGAGTATGTCATATACTCACCTAGCAATCATTCATCAGAGGAGGAGTTCTACAGTGATGCTGATGGTGTGGAAGATTAGGTGTAGCCCTGGTCAAGCTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.30% | 1.20% | 0.51% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 95.00% | 3.60% | 1.39% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.00% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 98.40% | 1.40% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 89.30% | 7.50% | 3.17% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.90% | 2.50% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1226733008 | C -> A | LOC_Os12g43034.1 | upstream_gene_variant ; 1369.0bp to feature; MODIFIER | silent_mutation | Average:33.292; most accessible tissue: Zhenshan97 flag leaf, score: 73.119 | N | N | N | N |
| vg1226733008 | C -> A | LOC_Os12g43050.1 | downstream_gene_variant ; 2721.0bp to feature; MODIFIER | silent_mutation | Average:33.292; most accessible tissue: Zhenshan97 flag leaf, score: 73.119 | N | N | N | N |
| vg1226733008 | C -> A | LOC_Os12g43034-LOC_Os12g43050 | intergenic_region ; MODIFIER | silent_mutation | Average:33.292; most accessible tissue: Zhenshan97 flag leaf, score: 73.119 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1226733008 | 3.87E-07 | 3.21E-08 | mr1871 | 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 |
| vg1226733008 | NA | 8.67E-08 | mr1951 | 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 |
| vg1226733008 | 1.99E-06 | NA | mr1871_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 |