| Variant ID: vg0135353524 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35353524 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 104. )
TTGGACACACGAAACACCTTTGTCCTCGAGTTCGGTGACTTACGGACCTTATGACCTGACAACGGTCACCACAACGACACTCCGGACGCTCACGCCACGT[G/A]
GGGAGTCCTAGGGGATTTACGTGCCATTCTAAAGCCTCAGCAGCAATTCGACGTTCATGCTCATCCTTCCACCTTAGGTAGTCCGATCTTGTTTCACTAC
GTAGTGAAACAAGATCGGACTACCTAAGGTGGAAGGATGAGCATGAACGTCGAATTGCTGCTGAGGCTTTAGAATGGCACGTAAATCCCCTAGGACTCCC[C/T]
ACGTGGCGTGAGCGTCCGGAGTGTCGTTGTGGTGACCGTTGTCAGGTCATAAGGTCCGTAAGTCACCGAACTCGAGGACAAAGGTGTTTCGTGTGTCCAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 24.10% | 11.80% | 0.61% | 63.46% | NA |
| All Indica | 2759 | 2.50% | 0.00% | 0.54% | 96.88% | NA |
| All Japonica | 1512 | 62.10% | 36.00% | 0.26% | 1.65% | NA |
| Aus | 269 | 0.70% | 0.00% | 3.72% | 95.54% | NA |
| Indica I | 595 | 4.20% | 0.00% | 1.18% | 94.62% | NA |
| Indica II | 465 | 0.20% | 0.20% | 0.00% | 99.57% | NA |
| Indica III | 913 | 1.10% | 0.00% | 0.22% | 98.69% | NA |
| Indica Intermediate | 786 | 4.30% | 0.00% | 0.76% | 94.91% | NA |
| Temperate Japonica | 767 | 55.00% | 43.40% | 0.26% | 1.30% | NA |
| Tropical Japonica | 504 | 63.50% | 33.90% | 0.40% | 2.18% | NA |
| Japonica Intermediate | 241 | 81.70% | 16.60% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 92.70% | 1.00% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 45.60% | 12.20% | 0.00% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135353524 | G -> A | LOC_Os01g61090.1 | synonymous_variant ; p.Pro1629Pro; LOW | synonymous_codon | Average:18.798; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
| vg0135353524 | G -> DEL | LOC_Os01g61090.1 | N | frameshift_variant | Average:18.798; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |