| Variant ID: vg0320572067 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 20572067 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 268. )
GCCGCTTGCATTCGCTACTCCGTCACCAAGAGACCAAGGATGGTGCAGGTAATTAAACTGAAATCATCCCTCAAGGGCCGTATCTATCGTTTCTGACATG[T/C]
TATCTTAAATAATCATTCAAAGATTTCAAGATGTATTAGATGTATCACTCCGACGAACATACAAGTCAACTTCTATTAGTTATAACAAAAATGATTTGAT
ATCAAATCATTTTTGTTATAACTAATAGAAGTTGACTTGTATGTTCGTCGGAGTGATACATCTAATACATCTTGAAATCTTTGAATGATTATTTAAGATA[A/G]
CATGTCAGAAACGATAGATACGGCCCTTGAGGGATGATTTCAGTTTAATTACCTGCACCATCCTTGGTCTCTTGGTGACGGAGTAGCGAATGCAAGCGGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.40% | 7.60% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 87.00% | 13.00% | 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 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 92.00% | 8.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 73.20% | 26.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 92.20% | 7.80% | 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 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0320572067 | T -> C | LOC_Os03g37110.1 | upstream_gene_variant ; 3544.0bp to feature; MODIFIER | silent_mutation | Average:71.49; most accessible tissue: Zhenshan97 panicle, score: 86.058 | N | N | N | N |
| vg0320572067 | T -> C | LOC_Os03g37130.1 | downstream_gene_variant ; 2174.0bp to feature; MODIFIER | silent_mutation | Average:71.49; most accessible tissue: Zhenshan97 panicle, score: 86.058 | N | N | N | N |
| vg0320572067 | T -> C | LOC_Os03g37120.1 | intron_variant ; MODIFIER | silent_mutation | Average:71.49; most accessible tissue: Zhenshan97 panicle, score: 86.058 | N | N | N | N |