| Variant ID: vg0430653732 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30653732 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 377. )
TGATGCCCATGTCTTCGCAGTAGTCGCCGAAGAGTTCACTAGTGAATTGGGTGCCATTATCCGTAATGATACGGTTAGGCACTCCAAAACGGGCCGTGAT[G/A]
CCCTTAATGAATTTAAGTGCAGAGTGCTTATCGATCTTGACGACCGGATAAGCCTCGGGCCACTTAGTGAACTTGTCGATCGCGACATACAGATACTCAA
TTGAGTATCTGTATGTCGCGATCGACAAGTTCACTAAGTGGCCCGAGGCTTATCCGGTCGTCAAGATCGATAAGCACTCTGCACTTAAATTCATTAAGGG[C/T]
ATCACGGCCCGTTTTGGAGTGCCTAACCGTATCATTACGGATAATGGCACCCAATTCACTAGTGAACTCTTCGGCGACTACTGCGAAGACATGGGCATCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.00% | 0.20% | 0.40% | 15.43% | NA |
| All Indica | 2759 | 98.80% | 0.30% | 0.22% | 0.69% | NA |
| All Japonica | 1512 | 55.80% | 0.00% | 0.46% | 43.78% | NA |
| Aus | 269 | 91.10% | 0.40% | 0.74% | 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 | 99.00% | 0.80% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 97.70% | 0.10% | 0.38% | 1.78% | NA |
| Temperate Japonica | 767 | 64.90% | 0.00% | 0.39% | 34.68% | NA |
| Tropical Japonica | 504 | 46.00% | 0.00% | 0.40% | 53.57% | NA |
| Japonica Intermediate | 241 | 46.90% | 0.00% | 0.83% | 52.28% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0430653732 | G -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0430653732 | G -> A | LOC_Os04g51730.1 | synonymous_variant ; p.Gly210Gly; LOW | synonymous_codon | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |