| Variant ID: vg0815411672 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 15411672 |
| 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: 222. )
GAGCTGCCTTCCTCTTACGGTTTATTTTGTTACAGTGCTCCTCCTGACGGATAGCCTTATCCACCAGCTTCTCAAAGTCCTCATAATCTCTAGAGATCAA[C/T]
TGGTTAGTCAATTCATCATCAAGACCAGACAGAAACTTCTCCTGCTTCTCGGCATCGGTACGCACGTCCTCAGGGGCGTAGCGCGCGAGGAGGTTGAACT
AGTTCAACCTCCTCGCGCGCTACGCCCCTGAGGACGTGCGTACCGATGCCGAGAAGCAGGAGAAGTTTCTGTCTGGTCTTGATGATGAATTGACTAACCA[G/A]
TTGATCTCTAGAGATTATGAGGACTTTGAGAAGCTGGTGGATAAGGCTATCCGTCAGGAGGAGCACTGTAACAAAATAAACCGTAAGAGGAAGGCAGCTC
| 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 | 18.50% | 0.80% | 6.96% | 73.72% | NA |
| All Indica | 2759 | 0.90% | 0.10% | 7.54% | 91.45% | NA |
| All Japonica | 1512 | 54.60% | 2.30% | 3.17% | 39.95% | NA |
| Aus | 269 | 0.40% | 0.00% | 24.54% | 75.09% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.50% | 99.50% | NA |
| Indica II | 465 | 1.50% | 0.00% | 5.59% | 92.90% | NA |
| Indica III | 913 | 0.70% | 0.10% | 13.14% | 86.09% | NA |
| Indica Intermediate | 786 | 1.70% | 0.10% | 7.51% | 90.71% | NA |
| Temperate Japonica | 767 | 83.20% | 0.00% | 0.78% | 16.04% | NA |
| Tropical Japonica | 504 | 16.10% | 6.70% | 6.75% | 70.44% | NA |
| Japonica Intermediate | 241 | 44.00% | 0.40% | 3.32% | 52.28% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 0.00% | 98.96% | NA |
| Intermediate | 90 | 22.20% | 3.30% | 7.78% | 66.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0815411672 | C -> T | LOC_Os08g25330.1 | synonymous_variant ; p.Gln238Gln; LOW | synonymous_codon | Average:4.366; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0815411672 | C -> DEL | LOC_Os08g25330.1 | N | frameshift_variant | Average:4.366; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |