| Variant ID: vg0721993476 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21993476 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 313. )
GCTGAAATACACACGCCTACACTCAACACTCCCCCTCAAGATGGGCGATAAATATCTATCATGCCCATCTTGCTACACGAAGAAGTGCACTCTCTAGCAC[C/T]
TAATGCCTTCGTTAAACTATCAGCTACTTGTTCACCAGAGTTTACAAAGCCTAAGTTTAAGGTTCCCTCATCCATTCTCTCTTTAATAAAGAAGCGATCT
AGATCGCTTCTTTATTAAAGAGAGAATGGATGAGGGAACCTTAAACTTAGGCTTTGTAAACTCTGGTGAACAAGTAGCTGATAGTTTAACGAAGGCATTA[G/A]
GTGCTAGAGAGTGCACTTCTTCGTGTAGCAAGATGGGCATGATAGATATTTATCGCCCATCTTGAGGGGGAGTGTTGAGTGTAGGCGTGTGTATTTCAGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.80% | 0.60% | 1.95% | 1.63% | NA |
| All Indica | 2759 | 99.50% | 0.10% | 0.36% | 0.04% | NA |
| All Japonica | 1512 | 92.50% | 0.00% | 2.45% | 5.03% | NA |
| Aus | 269 | 78.40% | 7.40% | 14.13% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.00% | 0.67% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.00% | 0.22% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.10% | 0.10% | 0.76% | 0.00% | NA |
| Temperate Japonica | 767 | 97.00% | 0.00% | 0.65% | 2.35% | NA |
| Tropical Japonica | 504 | 89.90% | 0.00% | 4.56% | 5.56% | NA |
| Japonica Intermediate | 241 | 83.80% | 0.00% | 3.73% | 12.45% | NA |
| VI/Aromatic | 96 | 85.40% | 8.30% | 6.25% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0721993476 | C -> DEL | LOC_Os07g36710.1 | N | frameshift_variant | Average:17.378; most accessible tissue: Callus, score: 32.482 | N | N | N | N |
| vg0721993476 | C -> T | LOC_Os07g36710.1 | missense_variant ; p.Gly783Ser; MODERATE | nonsynonymous_codon ; G783S | Average:17.378; most accessible tissue: Callus, score: 32.482 | unknown | unknown | TOLERATED | 0.97 |