| Variant ID: vg0409515258 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515258 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 291. )
CACCATCAAGCCCTTGCAACATATATGCCCCTTTAGACACAACATTATAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTGTTATC[C/T]
CGAGTTCCAATCGGCAAAATCAACTTCCATACAAGTTCACCTTCCGAAAAATCCTTAGGCACTACTTTCTTGTTATAATGCCTAGCAACTCGTTCCTTAT
ATAAGGAACGAGTTGCTAGGCATTATAACAAGAAAGTAGTGCCTAAGGATTTTTCGGAAGGTGAACTTGTATGGAAGTTGATTTTGCCGATTGGAACTCG[G/A]
GATAACAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTATAATGTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCTTGATGGTG
| 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 | 90.90% | 0.30% | 0.42% | 8.38% | NA |
| All Indica | 2759 | 99.60% | 0.30% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 74.30% | 0.10% | 0.73% | 24.87% | NA |
| Aus | 269 | 98.10% | 1.10% | 0.74% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.40% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.40% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 34.10% | 0.20% | 1.59% | 64.09% | NA |
| Japonica Intermediate | 241 | 80.90% | 0.40% | 1.24% | 17.43% | NA |
| VI/Aromatic | 96 | 75.00% | 2.10% | 3.12% | 19.79% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515258 | C -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:31.545; most accessible tissue: Minghui63 young leaf, score: 50.756 | N | N | N | N |
| vg0409515258 | C -> T | LOC_Os04g17380.1 | synonymous_variant ; p.Arg116Arg; LOW | synonymous_codon | Average:31.545; most accessible tissue: Minghui63 young leaf, score: 50.756 | N | N | N | N |