| Variant ID: vg1220960449 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960449 |
| 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: 300. )
CTTGTGTTCAATCGAAACAACCTCGCAAGCCTCACAAGGCATCTGAGGCGAGGAATTTGGCACCTCTAGAACTTGTTCATTCCGATTTGTGCGAAATGAA[C/T]
GGCGTGTTGACTAAAGGGGGAAAGAAATATTTCATGACACTGATAGATGATTGCACTAGATTTTGCTATGTGTATCTATTGAAAACAAAGGATGAGGCAT
ATGCCTCATCCTTTGTTTTCAATAGATACACATAGCAAAATCTAGTGCAATCATCTATCAGTGTCATGAAATATTTCTTTCCCCCTTTAGTCAACACGCC[G/A]
TTCATTTCGCACAAATCGGAATGAACAAGTTCTAGAGGTGCCAAATTCCTCGCCTCAGATGCCTTGTGAGGCTTGCGAGGTTGTTTCGATTGAACACAAG
| 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 | 59.10% | 0.10% | 0.40% | 40.39% | NA |
| All Indica | 2759 | 79.30% | 0.10% | 0.40% | 20.22% | NA |
| All Japonica | 1512 | 27.10% | 0.10% | 0.33% | 72.49% | NA |
| Aus | 269 | 52.00% | 0.00% | 0.74% | 47.21% | NA |
| Indica I | 595 | 63.70% | 0.00% | 0.67% | 35.63% | NA |
| Indica II | 465 | 79.10% | 0.00% | 0.22% | 20.65% | NA |
| Indica III | 913 | 88.60% | 0.20% | 0.22% | 10.95% | NA |
| Indica Intermediate | 786 | 80.40% | 0.00% | 0.51% | 19.08% | NA |
| Temperate Japonica | 767 | 10.40% | 0.00% | 0.26% | 89.31% | NA |
| Tropical Japonica | 504 | 48.20% | 0.40% | 0.60% | 50.79% | NA |
| Japonica Intermediate | 241 | 35.70% | 0.00% | 0.00% | 64.32% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 0.00% | 83.33% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 1.11% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960449 | C -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1220960449 | C -> T | LOC_Os12g34580.1 | synonymous_variant ; p.Asn611Asn; LOW | synonymous_codon | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |