| Variant ID: vg0112723170 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 12723170 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 191. )
GAACAAAGTCGTCCATCAATAACAATGAAGACACCAGTCGGCGGCGACGAAGGCGGTCGACGGTGAAAGCGAAGATGCCCACTAATGGCGGCATAATAGG[T/C]
CAGCCGTGTAAGCGGAAACACCAGTCGACGGCAACGAAGGTGAGCCAACGGTGACGATGTAGACATCCAACAACGGCGGCATAATAGGCCAGCCGTGTAG
CTACACGGCTGGCCTATTATGCCGCCGTTGTTGGATGTCTACATCGTCACCGTTGGCTCACCTTCGTTGCCGTCGACTGGTGTTTCCGCTTACACGGCTG[A/G]
CCTATTATGCCGCCATTAGTGGGCATCTTCGCTTTCACCGTCGACCGCCTTCGTCGCCGCCGACTGGTGTCTTCATTGTTATTGATGGACGACTTTGTTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.70% | 0.90% | 31.00% | 30.39% | NA |
| All Indica | 2759 | 7.70% | 0.10% | 44.29% | 47.84% | NA |
| All Japonica | 1512 | 96.10% | 0.00% | 2.25% | 1.65% | NA |
| Aus | 269 | 4.50% | 13.00% | 62.45% | 20.07% | NA |
| Indica I | 595 | 2.40% | 0.00% | 21.85% | 75.80% | NA |
| Indica II | 465 | 12.90% | 0.00% | 51.61% | 35.48% | NA |
| Indica III | 913 | 7.40% | 0.20% | 58.38% | 33.95% | NA |
| Indica Intermediate | 786 | 9.00% | 0.30% | 40.59% | 50.13% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 0.52% | 0.52% | NA |
| Tropical Japonica | 504 | 94.40% | 0.00% | 2.38% | 3.17% | NA |
| Japonica Intermediate | 241 | 90.50% | 0.00% | 7.47% | 2.07% | NA |
| VI/Aromatic | 96 | 54.20% | 3.10% | 18.75% | 23.96% | NA |
| Intermediate | 90 | 58.90% | 0.00% | 25.56% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0112723170 | T -> DEL | LOC_Os01g22620.1 | N | frameshift_variant | Average:16.957; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 | N | N | N | N |
| vg0112723170 | T -> C | LOC_Os01g22620.1 | missense_variant ; p.Asp420Gly; MODERATE | nonsynonymous_codon ; D420G | Average:16.957; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 | unknown | unknown | TOLERATED | 1.00 |