| Variant ID: vg0816101264 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 16101264 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GATGCTCCAGAGCCACCTTGGGGAGGCACAGAACTAATAAGTCCTGCACTAATTAATAATACACCCACGAATGGTTAGAGTGGAATAATATTAGTGAATA[T/C]
CACAAATACATCCACACAAGTTTGGAAGAATCATACCCTTTGAACTGGACATTATTTCTTCGCAAGGATCTTGTGGAGAAAGCTTCAAGTAATCGAATTT
AAATTCGATTACTTGAAGCTTTCTCCACAAGATCCTTGCGAAGAAATAATGTCCAGTTCAAAGGGTATGATTCTTCCAAACTTGTGTGGATGTATTTGTG[A/G]
TATTCACTAATATTATTCCACTCTAACCATTCGTGGGTGTATTATTAATTAGTGCAGGACTTATTAGTTCTGTGCCTCCCCAAGGTGGCTCTGGAGCATC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.40% | 24.40% | 19.26% | 2.96% | NA |
| All Indica | 2759 | 79.10% | 5.70% | 13.12% | 2.03% | NA |
| All Japonica | 1512 | 8.40% | 56.80% | 29.70% | 5.09% | NA |
| Aus | 269 | 65.10% | 3.00% | 30.11% | 1.86% | NA |
| Indica I | 595 | 69.90% | 13.30% | 14.79% | 2.02% | NA |
| Indica II | 465 | 75.10% | 5.20% | 16.13% | 3.66% | NA |
| Indica III | 913 | 87.80% | 1.20% | 9.86% | 1.10% | NA |
| Indica Intermediate | 786 | 78.40% | 5.60% | 13.87% | 2.16% | NA |
| Temperate Japonica | 767 | 1.60% | 96.30% | 1.83% | 0.26% | NA |
| Tropical Japonica | 504 | 16.90% | 6.30% | 69.05% | 7.74% | NA |
| Japonica Intermediate | 241 | 12.40% | 36.50% | 36.10% | 14.94% | NA |
| VI/Aromatic | 96 | 2.10% | 92.70% | 4.17% | 1.04% | NA |
| Intermediate | 90 | 42.20% | 41.10% | 15.56% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0816101264 | T -> C | LOC_Os08g26420.1 | upstream_gene_variant ; 4330.0bp to feature; MODIFIER | silent_mutation | Average:16.727; most accessible tissue: Callus, score: 48.963 | N | N | N | N |
| vg0816101264 | T -> C | LOC_Os08g26430.1 | upstream_gene_variant ; 2232.0bp to feature; MODIFIER | silent_mutation | Average:16.727; most accessible tissue: Callus, score: 48.963 | N | N | N | N |
| vg0816101264 | T -> C | LOC_Os08g26420-LOC_Os08g26430 | intergenic_region ; MODIFIER | silent_mutation | Average:16.727; most accessible tissue: Callus, score: 48.963 | N | N | N | N |
| vg0816101264 | T -> DEL | N | N | silent_mutation | Average:16.727; most accessible tissue: Callus, score: 48.963 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0816101264 | 5.14E-06 | NA | mr1362_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 |
| vg0816101264 | 4.29E-07 | 4.29E-07 | mr1581_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 |
| vg0816101264 | 1.76E-06 | 1.76E-06 | mr1852_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 |