| Variant ID: vg0524149426 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 24149426 |
| 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: 300. )
CCAAGCAACTGAGCTAAGACGATCGATTTCATATACTATGCCAGTAAACAGAAGTACGTAATGCTGAGATAATAATCATTGTCATTACTCATTAGCATTA[C/T]
CATTACGGCCAAGCTACTCTAATGCTAAGAAGCTCCAGGTCGACAGAGTCTGCACCGATCGACGCCGACGAGGCTTGCTTCCGGTGAAGAACCTGACGCC
GGCGTCAGGTTCTTCACCGGAAGCAAGCCTCGTCGGCGTCGATCGGTGCAGACTCTGTCGACCTGGAGCTTCTTAGCATTAGAGTAGCTTGGCCGTAATG[G/A]
TAATGCTAATGAGTAATGACAATGATTATTATCTCAGCATTACGTACTTCTGTTTACTGGCATAGTATATGAAATCGATCGTCTTAGCTCAGTTGCTTGG
| 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 | 99.80% | 0.10% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.20% | 0.11% | 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 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0524149426 | C -> T | LOC_Os05g41230.1 | 3_prime_UTR_variant ; 146.0bp to feature; MODIFIER | N | Average:75.5; most accessible tissue: Callus, score: 91.991 | N | N | N | N |
| vg0524149426 | C -> T | LOC_Os05g41240.1 | downstream_gene_variant ; 4307.0bp to feature; MODIFIER | N | Average:75.5; most accessible tissue: Callus, score: 91.991 | N | N | N | N |
| vg0524149426 | C -> T | LOC_Os05g41240.3 | downstream_gene_variant ; 4307.0bp to feature; MODIFIER | N | Average:75.5; most accessible tissue: Callus, score: 91.991 | N | N | N | N |
| vg0524149426 | C -> T | LOC_Os05g41240.2 | downstream_gene_variant ; 4307.0bp to feature; MODIFIER | N | Average:75.5; most accessible tissue: Callus, score: 91.991 | N | N | N | N |