| Variant ID: vg1220961662 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20961662 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 327. )
CGACACATACTCACCAGTTGCTCGCTTGACCACGATTCGAGTACTACTTGCTCTGGCAGCCTCTCATGGTCTTCTCATCCATCAGATGGACGTTAAGACA[G/T]
CTTTCCTAAACGGAGAGCTGGAGGAGGAGATCTATATGGATCAACCAGACGGGTATGTACTAGAAGGTCAGGAGGGAATGGTGTGTAAACTATTGAAATC
GATTTCAATAGTTTACACACCATTCCCTCCTGACCTTCTAGTACATACCCGTCTGGTTGATCCATATAGATCTCCTCCTCCAGCTCTCCGTTTAGGAAAG[C/A]
TGTCTTAACGTCCATCTGATGGATGAGAAGACCATGAGAGGCTGCCAGAGCAAGTAGTACTCGAATCGTGGTCAAGCGAGCAACTGGTGAGTATGTGTCG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.60% | 0.60% | 1.44% | 97.33% | NA |
| All Indica | 2759 | 1.10% | 0.30% | 1.81% | 96.85% | NA |
| All Japonica | 1512 | 0.00% | 1.20% | 1.19% | 97.62% | NA |
| Aus | 269 | 0.00% | 0.40% | 0.00% | 99.63% | NA |
| Indica I | 595 | 0.20% | 0.30% | 0.50% | 98.99% | NA |
| Indica II | 465 | 0.20% | 0.40% | 0.86% | 98.49% | NA |
| Indica III | 913 | 2.00% | 0.10% | 4.16% | 93.76% | NA |
| Indica Intermediate | 786 | 1.10% | 0.40% | 0.64% | 97.84% | NA |
| Temperate Japonica | 767 | 0.00% | 1.20% | 0.52% | 98.31% | NA |
| Tropical Japonica | 504 | 0.00% | 1.00% | 1.19% | 97.82% | NA |
| Japonica Intermediate | 241 | 0.00% | 1.70% | 3.32% | 95.02% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 1.10% | 1.10% | 0.00% | 97.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220961662 | G -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:6.695; most accessible tissue: Zhenshan97 flag leaf, score: 11.736 | N | N | N | N |
| vg1220961662 | G -> T | LOC_Os12g34580.1 | missense_variant ; p.Ala1016Ser; MODERATE | nonsynonymous_codon ; A1016S | Average:6.695; most accessible tissue: Zhenshan97 flag leaf, score: 11.736 | unknown | unknown | DELETERIOUS | 0.02 |