| Variant ID: vg0430653672 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30653672 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 368. )
CATTGGCGCGCTCCACTTGGCCATTGCTTCTGGGGTGGGCAGGTGAGGCGAAGCAGAGCTTGATGCCCATGTCTTCGCAGTAGTCGCCGAAGAGTTCACT[A/G]
GTGAATTGGGTGCCATTATCCGTAATGATACGGTTAGGCACTCCAAAACGGGCCGTGATGCCCTTAATGAATTTAAGTGCAGAGTGCTTATCGATCTTGA
TCAAGATCGATAAGCACTCTGCACTTAAATTCATTAAGGGCATCACGGCCCGTTTTGGAGTGCCTAACCGTATCATTACGGATAATGGCACCCAATTCAC[T/C]
AGTGAACTCTTCGGCGACTACTGCGAAGACATGGGCATCAAGCTCTGCTTCGCCTCACCTGCCCACCCCAGAAGCAATGGCCAAGTGGAGCGCGCCAATG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.60% | 0.70% | 7.64% | 17.05% | NA |
| All Indica | 2759 | 95.00% | 0.80% | 3.23% | 0.91% | NA |
| All Japonica | 1512 | 37.60% | 0.00% | 14.88% | 47.55% | NA |
| Aus | 269 | 74.00% | 3.70% | 10.41% | 11.90% | NA |
| Indica I | 595 | 98.00% | 0.20% | 1.51% | 0.34% | NA |
| Indica II | 465 | 93.80% | 0.90% | 4.52% | 0.86% | NA |
| Indica III | 913 | 96.30% | 1.00% | 2.63% | 0.11% | NA |
| Indica Intermediate | 786 | 92.10% | 1.10% | 4.45% | 2.29% | NA |
| Temperate Japonica | 767 | 38.90% | 0.00% | 21.12% | 40.03% | NA |
| Tropical Japonica | 504 | 35.50% | 0.00% | 8.13% | 56.35% | NA |
| Japonica Intermediate | 241 | 37.80% | 0.00% | 9.13% | 53.11% | NA |
| VI/Aromatic | 96 | 68.80% | 0.00% | 9.38% | 21.88% | NA |
| Intermediate | 90 | 77.80% | 1.10% | 11.11% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430653672 | A -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0430653672 | A -> G | LOC_Os04g51730.1 | synonymous_variant ; p.Thr230Thr; LOW | synonymous_codon | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |