| Variant ID: vg0131448546 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31448546 |
| 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: 99. )
AGGCCGCAGGGGAAAGGATGTTGAGGGCCGCTCCCCCATCAATGAGGACACGCCCCAACTTCACGTTGCAAACGGTGGGAGAAACCACCATCGCAATCTG[C/T]
CCTCCCCGGGCAACGCACGGTGGGTGGTCGGTCTGGTCGAAGGTGAGGGCAACCTCCGACCACCGCGCCCGGCGCGTCGCCTCATGAGTAGGGGCCGTGG
CCACGGCCCCTACTCATGAGGCGACGCGCCGGGCGCGGTGGTCGGAGGTTGCCCTCACCTTCGACCAGACCGACCACCCACCGTGCGTTGCCCGGGGAGG[G/A]
CAGATTGCGATGGTGGTTTCTCCCACCGTTTGCAACGTGAAGTTGGGGCGTGTCCTCATTGATGGGGGAGCGGCCCTCAACATCCTTTCCCCTGCGGCCT
| 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 | 33.70% | 3.90% | 17.48% | 44.94% | NA |
| All Indica | 2759 | 6.40% | 6.60% | 28.38% | 58.61% | NA |
| All Japonica | 1512 | 83.30% | 0.00% | 0.26% | 16.40% | NA |
| Aus | 269 | 1.10% | 0.00% | 10.41% | 88.48% | NA |
| Indica I | 595 | 10.90% | 4.00% | 48.57% | 36.47% | NA |
| Indica II | 465 | 3.40% | 4.70% | 18.06% | 73.76% | NA |
| Indica III | 913 | 1.60% | 11.00% | 21.80% | 65.61% | NA |
| Indica Intermediate | 786 | 10.20% | 4.70% | 26.84% | 58.27% | NA |
| Temperate Japonica | 767 | 87.90% | 0.00% | 0.13% | 11.99% | NA |
| Tropical Japonica | 504 | 90.30% | 0.00% | 0.60% | 9.13% | NA |
| Japonica Intermediate | 241 | 54.40% | 0.00% | 0.00% | 45.64% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 67.80% | 1.10% | 12.22% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131448546 | C -> T | LOC_Os01g54660.1 | synonymous_variant ; p.Gly609Gly; LOW | synonymous_codon | Average:21.067; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0131448546 | C -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:21.067; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |