| Variant ID: vg0801635532 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 1635532 |
| 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: 277. )
GGCGACGCTCGCCATGGCTGACCAGCACAGCACTACTGCGACGCGCTCAAGGATGTTTGTGTTCAGTTCATGGCCGTTGGGTTGGATGACCACAATTAAT[G/A]
ATTGATATTTGAATATGATACTAGTTGAGTGCCCGTGCCTTGCTACGGGGCAAAAAGTATGCATCCATTTTAAGTTACATTGAATAAAATAATGTTAAGT
ACTTAACATTATTTTATTCAATGTAACTTAAAATGGATGCATACTTTTTGCCCCGTAGCAAGGCACGGGCACTCAACTAGTATCATATTCAAATATCAAT[C/T]
ATTAATTGTGGTCATCCAACCCAACGGCCATGAACTGAACACAAACATCCTTGAGCGCGTCGCAGTAGTGCTGTGCTGGTCAGCCATGGCGAGCGTCGCC
| 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 | 97.50% | 1.90% | 0.25% | 0.40% | NA |
| All Indica | 2759 | 98.60% | 0.30% | 0.43% | 0.69% | NA |
| All Japonica | 1512 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.60% | 1.00% | 1.01% | 1.34% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.00% | 0.11% | 0.55% | NA |
| Indica Intermediate | 786 | 98.20% | 0.40% | 0.64% | 0.76% | NA |
| Temperate Japonica | 767 | 94.90% | 5.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 93.70% | 6.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0801635532 | G -> A | LOC_Os08g03490.1 | missense_variant ; p.Asp344Asn; MODERATE | nonsynonymous_codon ; D344N | Average:73.072; most accessible tissue: Minghui63 root, score: 81.505 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0801635532 | G -> DEL | LOC_Os08g03490.1 | N | frameshift_variant | Average:73.072; most accessible tissue: Minghui63 root, score: 81.505 | N | N | N | N |