| Variant ID: vg0424199421 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24199421 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.02, others allele: 0.00, population size: 209. )
TTGCGGCTTTCATGACCCGCCTTATGTACCCCATGAATATATTATTAGGTTGAAAGCCATGGATGGTGAGCTTGCTTAGGTTGGAGTGCTTGAAATCAGA[T/C]
GGTTCCCAGTTTATATTGCTCTTCTTGCAGATCACGAATCTCTTTATCAGCTCTTCCTCAACGGGTACACAGAGATGGTCCGTTGCCTACACAAATATAG
CTATATTTGTGTAGGCAACGGACCATCTCTGTGTACCCGTTGAGGAAGAGCTGATAAAGAGATTCGTGATCTGCAAGAAGAGCAATATAAACTGGGAACC[A/G]
TCTGATTTCAAGCACTCCAACCTAAGCAAGCTCACCATCCATGGCTTTCAACCTAATAATATATTCATGGGGTACATAAGGCGGGTCATGAAAGCCGCAA
| 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 | 96.80% | 1.80% | 0.08% | 1.29% | NA |
| All Indica | 2759 | 95.50% | 3.00% | 0.07% | 1.41% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 91.40% | 0.00% | 0.74% | 7.81% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 89.20% | 7.30% | 0.22% | 3.29% | NA |
| Indica Intermediate | 786 | 97.20% | 1.80% | 0.00% | 1.02% | 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% | 1.10% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424199421 | T -> C | LOC_Os04g40780.1 | synonymous_variant ; p.Pro336Pro; LOW | synonymous_codon | Average:40.596; most accessible tissue: Minghui63 root, score: 63.915 | N | N | N | N |
| vg0424199421 | T -> DEL | LOC_Os04g40780.1 | N | frameshift_variant | Average:40.596; most accessible tissue: Minghui63 root, score: 63.915 | N | N | N | N |