| Variant ID: vg0138753955 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 38753955 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )
AGGCATGCCTGGTTTTACAGCTTATGCTGGTTTCTATGAGATCTGCTCACCGAAGAAGGGCGAGTTTGTTTTTGTTTCGGCTGCATCAGGAGCAGTTGGG[C/T]
AAATTGTAGGACAACTCGCAAAGCTTCATGGATGCTATGTTGTGGGAAGTGCTGGAACAAATCAGAAAGTATTAACTTAAAACTGATAATTGCATTCATT
AATGAATGCAATTATCAGTTTTAAGTTAATACTTTCTGATTTGTTCCAGCACTTCCCACAACATAGCATCCATGAAGCTTTGCGAGTTGTCCTACAATTT[G/A]
CCCAACTGCTCCTGATGCAGCCGAAACAAAAACAAACTCGCCCTTCTTCGGTGAGCAGATCTCATAGAAACCAGCATAAGCTGTAAAACCAGGCATGCCT
| 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 | 99.40% | 0.20% | 0.34% | 0.00% | NA |
| All Indica | 2759 | 99.00% | 0.40% | 0.58% | 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 | 96.50% | 1.50% | 2.02% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.20% | 0.30% | 0.51% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0138753955 | C -> T | LOC_Os01g66720.1 | stop_gained ; p.Gln178*; HIGH | N | Average:45.511; most accessible tissue: Callus, score: 84.07 | N | N | N | N |
| vg0138753955 | C -> T | LOC_Os01g66710.1 | downstream_gene_variant ; 3187.0bp to feature; MODIFIER | N | Average:45.511; most accessible tissue: Callus, score: 84.07 | N | N | N | N |
| vg0138753955 | C -> T | LOC_Os01g66730.1 | downstream_gene_variant ; 1103.0bp to feature; MODIFIER | N | Average:45.511; most accessible tissue: Callus, score: 84.07 | N | N | N | N |