| Variant ID: vg0508169154 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 8169154 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGTCTGCATCTGTCAAGGAGGCCATCAAGCTATCGGACTATGAGCGAACGCTGAAGAAAGCATCTTCTGGAAAGTCCAAACCAGTCCCTCAGCTTGGAGA[G/A]
CAACCAAACCAGGAGATCGAGCCGTTGGTGACCGGTAAAGAAATGATGATAGAATAATTTATTACTGACACCGGTCTAACTACGAATCAATTGCTAGGAG
CTCCTAGCAATTGATTCGTAGTTAGACCGGTGTCAGTAATAAATTATTCTATCATCATTTCTTTACCGGTCACCAACGGCTCGATCTCCTGGTTTGGTTG[C/T]
TCTCCAAGCTGAGGGACTGGTTTGGACTTTCCAGAAGATGCTTTCTTCAGCGTTCGCTCATAGTCCGATAGCTTGATGGCCTCCTTGACAGATGCAGACA
| 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 | 49.10% | 0.30% | 13.61% | 36.99% | NA |
| All Indica | 2759 | 26.00% | 0.00% | 18.85% | 55.13% | NA |
| All Japonica | 1512 | 91.80% | 0.90% | 3.24% | 4.03% | NA |
| Aus | 269 | 21.60% | 0.00% | 24.91% | 53.53% | NA |
| Indica I | 595 | 32.60% | 0.00% | 6.39% | 61.01% | NA |
| Indica II | 465 | 30.80% | 0.00% | 17.20% | 52.04% | NA |
| Indica III | 913 | 16.20% | 0.00% | 32.97% | 50.82% | NA |
| Indica Intermediate | 786 | 29.60% | 0.00% | 12.85% | 57.51% | NA |
| Temperate Japonica | 767 | 89.80% | 1.70% | 4.69% | 3.78% | NA |
| Tropical Japonica | 504 | 98.40% | 0.00% | 0.20% | 1.39% | NA |
| Japonica Intermediate | 241 | 84.20% | 0.40% | 4.98% | 10.37% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 72.20% | 0.00% | 4.44% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0508169154 | G -> DEL | LOC_Os05g14460.1 | N | frameshift_variant | Average:8.563; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 | N | N | N | N |
| vg0508169154 | G -> A | LOC_Os05g14460.1 | synonymous_variant ; p.Glu716Glu; LOW | synonymous_codon | Average:8.563; most accessible tissue: Zhenshan97 flag leaf, score: 13.342 | N | N | N | N |