| Variant ID: vg0801634656 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 1634656 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, T: 0.08, others allele: 0.00, population size: 99. )
GACGCGGACGGCGCGCGCCACGCACCAGTTCGAGATCGTCGGGTACAGCCTCAAGAGGTGCCTCGCCGCCGGCGAGTTCGTCCGGTCCTCCGCCTTCGCC[G/T]
CCTGCGGCTACAGGTGGTCCGTCCGCGTCTACCCCGGCGGGTTCGGGCCGGCGCACCGGGAGTTCGTGTCGGTGTTCGTCAAGATGATGACCAACAGGGG
CCCCTGTTGGTCATCATCTTGACGAACACCGACACGAACTCCCGGTGCGCCGGCCCGAACCCGCCGGGGTAGACGCGGACGGACCACCTGTAGCCGCAGG[C/A]
GGCGAAGGCGGAGGACCGGACGAACTCGCCGGCGGCGAGGCACCTCTTGAGGCTGTACCCGACGATCTCGAACTGGTGCGTGGCGCGCGCCGTCCGCGTC
| 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 | 49.90% | 49.20% | 0.11% | 0.78% | NA |
| All Indica | 2759 | 80.70% | 17.80% | 0.14% | 1.34% | NA |
| All Japonica | 1512 | 2.30% | 97.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 19.00% | 81.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.50% | 2.00% | 0.00% | 2.52% | NA |
| Indica II | 465 | 88.40% | 11.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 71.10% | 28.00% | 0.11% | 0.77% | NA |
| Indica Intermediate | 786 | 76.20% | 21.50% | 0.38% | 1.91% | NA |
| Temperate Japonica | 767 | 3.10% | 96.90% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.50% | 97.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 6.20% | 93.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 43.30% | 55.60% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0801634656 | G -> T | LOC_Os08g03490.1 | missense_variant ; p.Ala52Ser; MODERATE | nonsynonymous_codon ; A52S | Average:76.126; most accessible tissue: Minghui63 flag leaf, score: 83.197 | unknown | unknown | DELETERIOUS | 0.02 |
| vg0801634656 | G -> DEL | LOC_Os08g03490.1 | N | frameshift_variant | Average:76.126; most accessible tissue: Minghui63 flag leaf, score: 83.197 | N | N | N | N |