| Variant ID: vg1001932749 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1932749 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.89, C: 0.11, others allele: 0.00, population size: 74. )
TGCTATTTGTATAGCAAGATAATTGTTGTACATAGTACTCTTATTTTACTATAAAATATCACTATGTGTTACCAAATCAACTGGTGCTTCGGCGCTTCCT[T/C]
GTAGTTGTTGTAGATCCATTCTTGTCATGAAATAAAGCTGTAGCAGAAGATACATACTTAGTATAAGGTGATATTCGTGATTCCCACGTTGCTATTTCAA
TTGAAATAGCAACGTGGGAATCACGAATATCACCTTATACTAAGTATGTATCTTCTGCTACAGCTTTATTTCATGACAAGAATGGATCTACAACAACTAC[A/G]
AGGAAGCGCCGAAGCACCAGTTGATTTGGTAACACATAGTGATATTTTATAGTAAAATAAGAGTACTATGTACAACAATTATCTTGCTATACAAATAGCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.90% | 32.70% | 0.74% | 15.70% | NA |
| All Indica | 2759 | 22.80% | 53.50% | 1.20% | 22.51% | NA |
| All Japonica | 1512 | 96.30% | 3.10% | 0.00% | 0.60% | NA |
| Aus | 269 | 59.90% | 1.50% | 0.74% | 37.92% | NA |
| Indica I | 595 | 3.70% | 54.10% | 1.68% | 40.50% | NA |
| Indica II | 465 | 20.20% | 63.70% | 1.08% | 15.05% | NA |
| Indica III | 913 | 32.40% | 47.40% | 0.44% | 19.72% | NA |
| Indica Intermediate | 786 | 27.50% | 54.20% | 1.78% | 16.54% | NA |
| Temperate Japonica | 767 | 98.60% | 0.50% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.70% | 2.50% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 75.60% | 17.80% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001932749 | T -> C | LOC_Os10g04160.1 | missense_variant ; p.Gln345Arg; MODERATE | nonsynonymous_codon ; Q345R | Average:34.343; most accessible tissue: Callus, score: 65.274 | unknown | unknown | TOLERATED | 0.11 |
| vg1001932749 | T -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:34.343; most accessible tissue: Callus, score: 65.274 | N | N | N | N |