| Variant ID: vg0424676968 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24676968 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 122. )
CCGATAGCTTGATGGCCTCCTTGACAGATGCAGACATACCCCTGAAGAAGTTCCTGACACTGGGGTCTATAGGAATCTTCTTTTCTGGACTTCGAGGCTT[G/A]
AATTGTCTCTTGACTTCTGATGCAACGTAAGCGTCAAGCTCCTTTTGCGTGCAATCGTACCCCGGGTCCTTGTTCTTGGCGGCGTCAACTTTCGCCTTCT
AGAAGGCGAAAGTTGACGCCGCCAAGAACAAGGACCCGGGGTACGATTGCACGCAAAAGGAGCTTGACGCTTACGTTGCATCAGAAGTCAAGAGACAATT[C/T]
AAGCCTCGAAGTCCAGAAAAGAAGATTCCTATAGACCCCAGTGTCAGGAACTTCTTCAGGGGTATGTCTGCATCTGTCAAGGAGGCCATCAAGCTATCGG
| 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 | 16.10% | 0.10% | 0.89% | 82.92% | NA |
| All Indica | 2759 | 1.10% | 0.20% | 0.25% | 98.48% | NA |
| All Japonica | 1512 | 42.90% | 0.00% | 2.12% | 55.03% | NA |
| Aus | 269 | 1.50% | 0.40% | 0.00% | 98.14% | NA |
| Indica I | 595 | 2.40% | 0.00% | 0.17% | 97.48% | NA |
| Indica II | 465 | 0.20% | 0.20% | 0.00% | 99.57% | NA |
| Indica III | 913 | 0.20% | 0.20% | 0.33% | 99.23% | NA |
| Indica Intermediate | 786 | 1.70% | 0.30% | 0.38% | 97.71% | NA |
| Temperate Japonica | 767 | 76.30% | 0.00% | 1.30% | 22.43% | NA |
| Tropical Japonica | 504 | 2.00% | 0.00% | 2.58% | 95.44% | NA |
| Japonica Intermediate | 241 | 22.00% | 0.00% | 3.73% | 74.27% | NA |
| VI/Aromatic | 96 | 68.80% | 0.00% | 1.04% | 30.21% | NA |
| Intermediate | 90 | 12.20% | 0.00% | 2.22% | 85.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424676968 | G -> DEL | LOC_Os04g41599.1 | N | frameshift_variant | Average:6.526; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0424676968 | G -> A | LOC_Os04g41599.1 | synonymous_variant ; p.Phe1560Phe; LOW | synonymous_codon | Average:6.526; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |