| Variant ID: vg1012223994 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12223994 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CCAGGAGCGACCAATGGCGCGGATGCGGACACGGTCGGGGAGGGAGCGCGAGGACGGCGGCGTGGAGCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGC[A/G]
ACGGCGGTGCGGAGCGCGAGCAGGATGTGGCCGTGCGCGAGAAGGCTGTTGAACGCTGGCCGGTACGAGGCTTGCTGCGGCCGCTGGTCGCTGGGTCTCG
CGAGACCCAGCGACCAGCGGCCGCAGCAAGCCTCGTACCGGCCAGCGTTCAACAGCCTTCTCGCGCACGGCCACATCCTGCTCGCGCTCCGCACCGCCGT[T/C]
GCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGCTCCACGCCGCCGTCCTCGCGCTCCCTCCCCGACCGTGTCCGCATCCGCGCCATTGGTCGCTCCTGG
| 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 | 49.00% | 0.20% | 1.25% | 49.49% | NA |
| All Indica | 2759 | 32.10% | 0.20% | 1.74% | 65.93% | NA |
| All Japonica | 1512 | 88.50% | 0.10% | 0.00% | 11.38% | NA |
| Aus | 269 | 11.20% | 0.70% | 2.60% | 85.50% | NA |
| Indica I | 595 | 12.60% | 0.30% | 2.18% | 84.87% | NA |
| Indica II | 465 | 40.20% | 0.00% | 2.58% | 57.20% | NA |
| Indica III | 913 | 36.00% | 0.30% | 1.10% | 62.54% | NA |
| Indica Intermediate | 786 | 37.50% | 0.10% | 1.65% | 60.69% | NA |
| Temperate Japonica | 767 | 95.60% | 0.00% | 0.00% | 4.43% | NA |
| Tropical Japonica | 504 | 81.90% | 0.00% | 0.00% | 18.06% | NA |
| Japonica Intermediate | 241 | 79.70% | 0.80% | 0.00% | 19.50% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 2.08% | 88.54% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 2.22% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012223994 | A -> G | LOC_Os10g23830.1 | missense_variant ; p.Asn30Asp; MODERATE | nonsynonymous_codon | Average:13.537; most accessible tissue: Callus, score: 51.074 | unknown | unknown | TOLERATED | 0.84 |
| vg1012223994 | A -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:13.537; most accessible tissue: Callus, score: 51.074 | N | N | N | N |