| Variant ID: vg0118270473 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 18270473 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 304. )
AGGTTGCGGTGCGAGAGATTACTACGCACTGGTTTGAGGACCAGCGAACGTGTAGAATTATCTCTCGGACACCAATGGAGGTTGCGGTACGAGAGATTGC[T/A]
ACGCACTGGTTCGAGGACCAGCGAGCGAGTAGAATCATCTCTCAAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGC
GCTGGTTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTTGAGAGATGATTCTACTCGCTCGCTGGTCCTCGAACCAGTGCGT[A/T]
GCAATCTCTCGTACCGCAACCTCCATTGGTGTCCGAGAGATAATTCTACACGTTCGCTGGTCCTCAAACCAGTGCGTAGTAATCTCTCGCACCGCAACCT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 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 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270473 | T -> A | LOC_Os01g33180.1 | synonymous_variant ; p.Ala9Ala; LOW | N | Average:53.726; most accessible tissue: Minghui63 young leaf, score: 75.479 | N | N | N | N |
| vg0118270473 | T -> A | LOC_Os01g33160.1 | downstream_gene_variant ; 3275.0bp to feature; MODIFIER | N | Average:53.726; most accessible tissue: Minghui63 young leaf, score: 75.479 | N | N | N | N |
| vg0118270473 | T -> A | LOC_Os01g33190.1 | downstream_gene_variant ; 2010.0bp to feature; MODIFIER | N | Average:53.726; most accessible tissue: Minghui63 young leaf, score: 75.479 | N | N | N | N |