| Variant ID: vg0222052160 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 22052160 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GAGGCTGGCACCGTCCTGGACGATGGCGCCAGCCACTCTGACGTCCCAAAAAGGACCATTTTTGGGATAAGTTTTTCTAGGGGTCTATTTGCGAAATAAG[T/C]
TTTTCAAAAAGACCAAAATGTGAAAAATCCAGAAGAATACGCCATCTGAAAAAAAAGGCCGATAAAAATGCCATAAAAAATAGCGAAAAAGAAGTCTGAT
ATCAGACTTCTTTTTCGCTATTTTTTATGGCATTTTTATCGGCCTTTTTTTTCAGATGGCGTATTCTTCTGGATTTTTCACATTTTGGTCTTTTTGAAAA[A/G]
CTTATTTCGCAAATAGACCCCTAGAAAAACTTATCCCAAAAATGGTCCTTTTTGGGACGTCAGAGTGGCTGGCGCCATCGTCCAGGACGGTGCCAGCCTC
| 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 | 52.40% | 35.40% | 0.63% | 11.51% | NA |
| All Indica | 2759 | 74.60% | 5.90% | 0.91% | 18.59% | NA |
| All Japonica | 1512 | 7.70% | 91.80% | 0.00% | 0.46% | NA |
| Aus | 269 | 92.60% | 1.50% | 1.12% | 4.83% | NA |
| Indica I | 595 | 71.60% | 3.00% | 0.84% | 24.54% | NA |
| Indica II | 465 | 67.30% | 1.70% | 1.08% | 29.89% | NA |
| Indica III | 913 | 83.20% | 8.10% | 0.66% | 8.00% | NA |
| Indica Intermediate | 786 | 71.20% | 7.90% | 1.15% | 19.72% | NA |
| Temperate Japonica | 767 | 1.20% | 98.40% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 19.40% | 80.20% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 4.10% | 95.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 11.50% | 87.50% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 45.60% | 41.10% | 2.22% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0222052160 | T -> DEL | N | N | silent_mutation | Average:23.65; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0222052160 | T -> C | LOC_Os02g36510.1 | upstream_gene_variant ; 4768.0bp to feature; MODIFIER | silent_mutation | Average:23.65; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0222052160 | T -> C | LOC_Os02g36505.1 | downstream_gene_variant ; 1778.0bp to feature; MODIFIER | silent_mutation | Average:23.65; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0222052160 | T -> C | LOC_Os02g36500-LOC_Os02g36505 | intergenic_region ; MODIFIER | silent_mutation | Average:23.65; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0222052160 | NA | 6.14E-09 | Awn_length | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0222052160 | NA | 2.45E-28 | mr1075 | 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 |
| vg0222052160 | 6.08E-07 | 6.08E-07 | mr1388 | 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 |