| Variant ID: vg0521979295 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 21979295 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 295. )
TGAAAAGAAGAAAAGAAGTAGGGATTGAGAAGAAGAACACAACCAATGAGTGTGAGTCCGTTGAAGAAGAAAACCAAGTCATTGATCATGAGGATGAAGT[G/T]
CCCTTTCCTCGTAGGTTTTGCCACACATGCCACGAAGCTGGTCATAATTCGCGGACTTGTGGCCGGACATCTACGTACAAGAGAAAACTTTAGAATATGG
CCATATTCTAAAGTTTTCTCTTGTACGTAGATGTCCGGCCACAAGTCCGCGAATTATGACCAGCTTCGTGGCATGTGTGGCAAAACCTACGAGGAAAGGG[C/A]
ACTTCATCCTCATGATCAATGACTTGGTTTTCTTCTTCAACGGACTCACACTCATTGGTTGTGTTCTTCTTCTCAATCCCTACTTCTTTTCTTCTTTTCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.70% | 0.80% | 15.07% | 1.50% | NA |
| All Indica | 2759 | 81.90% | 1.30% | 14.35% | 2.46% | NA |
| All Japonica | 1512 | 84.90% | 0.00% | 14.95% | 0.20% | NA |
| Aus | 269 | 92.90% | 0.00% | 7.06% | 0.00% | NA |
| Indica I | 595 | 75.60% | 0.00% | 21.85% | 2.52% | NA |
| Indica II | 465 | 96.10% | 0.00% | 3.87% | 0.00% | NA |
| Indica III | 913 | 75.20% | 3.90% | 16.54% | 4.27% | NA |
| Indica Intermediate | 786 | 85.90% | 0.00% | 12.34% | 1.78% | NA |
| Temperate Japonica | 767 | 97.30% | 0.00% | 2.35% | 0.39% | NA |
| Tropical Japonica | 504 | 66.70% | 0.00% | 33.33% | 0.00% | NA |
| Japonica Intermediate | 241 | 83.40% | 0.00% | 16.60% | 0.00% | NA |
| VI/Aromatic | 96 | 40.60% | 0.00% | 59.38% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 0.00% | 15.56% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0521979295 | G -> T | LOC_Os05g37540.1 | synonymous_variant ; p.Val792Val; LOW | synonymous_codon | Average:9.123; most accessible tissue: Zhenshan97 flag leaf, score: 15.873 | N | N | N | N |
| vg0521979295 | G -> DEL | LOC_Os05g37540.1 | N | frameshift_variant | Average:9.123; most accessible tissue: Zhenshan97 flag leaf, score: 15.873 | N | N | N | N |