| Variant ID: vg0430653708 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30653708 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 350. )
GGGCAGGTGAGGCGAAGCAGAGCTTGATGCCCATGTCTTCGCAGTAGTCGCCGAAGAGTTCACTAGTGAATTGGGTGCCATTATCCGTAATGATACGGTT[A/T]
GGCACTCCAAAACGGGCCGTGATGCCCTTAATGAATTTAAGTGCAGAGTGCTTATCGATCTTGACGACCGGATAAGCCTCGGGCCACTTAGTGAACTTGT
ACAAGTTCACTAAGTGGCCCGAGGCTTATCCGGTCGTCAAGATCGATAAGCACTCTGCACTTAAATTCATTAAGGGCATCACGGCCCGTTTTGGAGTGCC[T/A]
AACCGTATCATTACGGATAATGGCACCCAATTCACTAGTGAACTCTTCGGCGACTACTGCGAAGACATGGGCATCAAGCTCTGCTTCGCCTCACCTGCCC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.20% | 0.00% | 0.51% | 15.26% | NA |
| All Indica | 2759 | 99.10% | 0.00% | 0.18% | 0.69% | NA |
| All Japonica | 1512 | 55.80% | 0.00% | 0.99% | 43.25% | NA |
| Aus | 269 | 92.20% | 0.00% | 0.00% | 7.81% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 98.90% | 0.00% | 0.43% | 0.65% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 97.80% | 0.00% | 0.38% | 1.78% | NA |
| Temperate Japonica | 767 | 65.10% | 0.00% | 0.78% | 34.16% | NA |
| Tropical Japonica | 504 | 46.00% | 0.00% | 0.40% | 53.57% | NA |
| Japonica Intermediate | 241 | 46.50% | 0.00% | 2.90% | 50.62% | NA |
| VI/Aromatic | 96 | 77.10% | 1.00% | 3.12% | 18.75% | NA |
| Intermediate | 90 | 88.90% | 0.00% | 1.11% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430653708 | A -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0430653708 | A -> T | LOC_Os04g51730.1 | synonymous_variant ; p.Pro218Pro; LOW | synonymous_codon | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |