| Variant ID: vg0430654095 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30654095 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 404. )
GAGCTGTCGGCCAATAGAACCCTTGACGAAAGGCCTTGCCAACCAAGGTGCGCGAGGCGGAATGGGCTCCGCACTCGCCTTCATGGATATCGGCAAGAAG[C/T]
TCAACGCCTTGTTCCTGAGGAATGCACTTCAGGAGGATTCCGTTAGCCGCGCGCCGATAGAGGGTCCCTTCTATCAGCACGTAGCGTTTGGAAATGCGTT
AACGCATTTCCAAACGCTACGTGCTGATAGAAGGGACCCTCTATCGGCGCGCGGCTAACGGAATCCTCCTGAAGTGCATTCCTCAGGAACAAGGCGTTGA[G/A]
CTTCTTGCCGATATCCATGAAGGCGAGTGCGGAGCCCATTCCGCCTCGCGCACCTTGGTTGGCAAGGCCTTTCGTCAAGGGTTCTATTGGCCGACAGCTC
| 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 | 84.50% | 0.20% | 0.42% | 14.92% | NA |
| All Indica | 2759 | 99.30% | 0.10% | 0.00% | 0.62% | NA |
| All Japonica | 1512 | 56.30% | 0.10% | 1.12% | 42.46% | NA |
| Aus | 269 | 90.70% | 1.10% | 0.74% | 7.43% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.00% | 0.43% | NA |
| Indica III | 913 | 99.80% | 0.10% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 98.20% | 0.10% | 0.00% | 1.65% | NA |
| Temperate Japonica | 767 | 65.40% | 0.10% | 0.39% | 34.03% | NA |
| Tropical Japonica | 504 | 46.20% | 0.00% | 1.98% | 51.79% | NA |
| Japonica Intermediate | 241 | 48.10% | 0.40% | 1.66% | 49.79% | NA |
| VI/Aromatic | 96 | 78.10% | 2.10% | 1.04% | 18.75% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430654095 | C -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 | N | N | N | N |
| vg0430654095 | C -> T | LOC_Os04g51730.1 | synonymous_variant ; p.Glu89Glu; LOW | synonymous_codon | Average:9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 | N | N | N | N |