| Variant ID: vg0602082808 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 2082808 |
| 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: 277. )
TGATGTTTCGGTGATACTTCTCCACCCCTTGTAAGTAGCACTTGTGCTCGGTCACAATGCTAACTTTCCAATAATCATTCCATTTACCCTTATATGCATG[G/A]
ACACGCCATGGACAATCTTCCTTCATGCACCTCACTTCATACACATAATTTGTTGACTTGACCACCCTAAACTCTCTCTGCAATGAAACTGCCCAATGCT
AGCATTGGGCAGTTTCATTGCAGAGAGAGTTTAGGGTGGTCAAGTCAACAAATTATGTGTATGAAGTGAGGTGCATGAAGGAAGATTGTCCATGGCGTGT[C/T]
CATGCATATAAGGGTAAATGGAATGATTATTGGAAAGTTAGCATTGTGACCGAGCACAAGTGCTACTTACAAGGGGTGGAGAAGTATCACCGAAACATCA
| 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 | 0.50% | 0.20% | 1.21% | 98.05% | NA |
| All Indica | 2759 | 0.70% | 0.10% | 0.18% | 98.99% | NA |
| All Japonica | 1512 | 0.20% | 0.40% | 1.06% | 98.35% | NA |
| Aus | 269 | 1.10% | 0.00% | 12.64% | 86.25% | NA |
| Indica I | 595 | 0.70% | 0.50% | 0.34% | 98.49% | NA |
| Indica II | 465 | 0.90% | 0.00% | 0.22% | 98.92% | NA |
| Indica III | 913 | 0.50% | 0.10% | 0.00% | 99.34% | NA |
| Indica Intermediate | 786 | 0.80% | 0.00% | 0.25% | 98.98% | NA |
| Temperate Japonica | 767 | 0.10% | 0.80% | 1.04% | 98.04% | NA |
| Tropical Japonica | 504 | 0.40% | 0.00% | 1.59% | 98.02% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 2.22% | 97.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0602082808 | G -> A | LOC_Os06g04770.1 | synonymous_variant ; p.Val268Val; LOW | synonymous_codon | Average:24.467; most accessible tissue: Minghui63 young leaf, score: 49.581 | N | N | N | N |
| vg0602082808 | G -> DEL | LOC_Os06g04770.1 | N | frameshift_variant | Average:24.467; most accessible tissue: Minghui63 young leaf, score: 49.581 | N | N | N | N |