| Variant ID: vg0609242368 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9242368 |
| 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: 84. )
CCATCGCAACCTGCCCTCCCCGGGCAATGCACGGTGGGTGGTCAGTCTGGTCGAAAGTGAGAGCGACCTCCGACCACCGCGCCCGACGCATCGCCTCATG[G/A]
GTAGGGGCCATGGCCAGAAGCTCTCGTTTCATAGCCTTGAAGCTCCGGCGAGAGACGTGAGCACACGCTCCTCCATCGACGGTGGCAATGGTGGCCCCAG
CTGGGGCCACCATTGCCACCGTCGATGGAGGAGCGTGTGCTCACGTCTCTCGCCGGAGCTTCAAGGCTATGAAACGAGAGCTTCTGGCCATGGCCCCTAC[C/T]
CATGAGGCGATGCGTCGGGCGCGGTGGTCGGAGGTCGCTCTCACTTTCGACCAGACTGACCACCCACCGTGCATTGCCCGGGGAGGGCAGGTTGCGATGG
| 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 | 12.40% | 0.10% | 3.07% | 84.38% | NA |
| All Indica | 2759 | 1.10% | 0.20% | 0.91% | 97.75% | NA |
| All Japonica | 1512 | 36.20% | 0.00% | 0.53% | 63.29% | NA |
| Aus | 269 | 0.00% | 0.00% | 39.78% | 60.22% | NA |
| Indica I | 595 | 1.30% | 0.00% | 0.34% | 98.32% | NA |
| Indica II | 465 | 1.30% | 0.20% | 0.43% | 98.06% | NA |
| Indica III | 913 | 0.10% | 0.30% | 0.55% | 99.01% | NA |
| Indica Intermediate | 786 | 2.00% | 0.30% | 2.04% | 95.67% | NA |
| Temperate Japonica | 767 | 67.70% | 0.00% | 0.39% | 31.94% | NA |
| Tropical Japonica | 504 | 1.60% | 0.00% | 0.20% | 98.21% | NA |
| Japonica Intermediate | 241 | 8.30% | 0.00% | 1.66% | 90.04% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 3.12% | 96.88% | NA |
| Intermediate | 90 | 10.00% | 0.00% | 2.22% | 87.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609242368 | G -> A | LOC_Os06g16230.1 | synonymous_variant ; p.Thr581Thr; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0609242368 | G -> DEL | LOC_Os06g16230.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |