| Variant ID: vg0136199233 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36199233 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AATGAATCTAGACACACGTATATGTCTATATTCATTAGTATATATATAAATATGAGCAGTGCTAGAAAGTCTTATAATATAAAATAGAGGAAGTAATCTA[G/A]
TACTCTGTACTAGATGCATTCTAGTATTAGATGTGAGCATATATATATATATATATATATATATATAGAGAGAGAGAGAGAGAATTTTTATGGTACTATA
TATAGTACCATAAAAATTCTCTCTCTCTCTCTCTATATATATATATATATATATATATATATGCTCACATCTAATACTAGAATGCATCTAGTACAGAGTA[C/T]
TAGATTACTTCCTCTATTTTATATTATAAGACTTTCTAGCACTGCTCATATTTATATATATACTAATGAATATAGACATATACGTGTGTCTAGATTCATT
| 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 | 88.10% | 10.70% | 1.21% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 63.80% | 32.50% | 3.70% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 62.80% | 31.30% | 5.87% | 0.00% | NA |
| Tropical Japonica | 504 | 57.70% | 40.10% | 2.18% | 0.00% | NA |
| Japonica Intermediate | 241 | 79.30% | 20.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 12.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0136199233 | G -> A | LOC_Os01g62514.1 | upstream_gene_variant ; 4622.0bp to feature; MODIFIER | silent_mutation | Average:49.834; most accessible tissue: Callus, score: 70.147 | N | N | N | N |
| vg0136199233 | G -> A | LOC_Os01g62514-LOC_Os01g62520 | intergenic_region ; MODIFIER | silent_mutation | Average:49.834; most accessible tissue: Callus, score: 70.147 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0136199233 | 8.78E-06 | NA | mr1035_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 |
| vg0136199233 | 1.16E-06 | NA | mr1631_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 |
| vg0136199233 | NA | 8.62E-07 | mr1631_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 |
| vg0136199233 | NA | 3.12E-11 | mr1806_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 |