| Variant ID: vg1109585484 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9585484 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 409. )
TGCTAGCATCAGTAGCACCGAATTTAGTATTCAGTGCATCCCACAACTTCTTAGCGTCGGTCATATGCATATACACCTCGACCAGACGATCGCCAAGAAC[G/A]
CTAAGAATGCATCCCACAAAGAGAGTAGTGGCTTCCTCGAATTGCTTCTGCTGTTCAGCAGTAAGAACTCCTTCAGGTTTGCCAGTACTCACCCAGAAGC
GCTTCTGGGTGAGTACTGGCAAACCTGAAGGAGTTCTTACTGCTGAACAGCAGAAGCAATTCGAGGAAGCCACTACTCTCTTTGTGGGATGCATTCTTAG[C/T]
GTTCTTGGCGATCGTCTGGTCGAGGTGTATATGCATATGACCGACGCTAAGAAGTTGTGGGATGCACTGAATACTAAATTCGGTGCTACTGATGCTAGCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.00% | 4.90% | 22.49% | 5.54% | NA |
| All Indica | 2759 | 96.30% | 0.90% | 2.25% | 0.54% | NA |
| All Japonica | 1512 | 7.80% | 13.40% | 62.63% | 16.14% | NA |
| Aus | 269 | 96.30% | 1.10% | 2.60% | 0.00% | NA |
| Indica I | 595 | 95.10% | 0.00% | 3.36% | 1.51% | NA |
| Indica II | 465 | 97.60% | 0.40% | 1.29% | 0.65% | NA |
| Indica III | 913 | 96.50% | 1.80% | 1.64% | 0.11% | NA |
| Indica Intermediate | 786 | 96.30% | 0.80% | 2.67% | 0.25% | NA |
| Temperate Japonica | 767 | 6.90% | 7.40% | 64.93% | 20.73% | NA |
| Tropical Japonica | 504 | 7.70% | 24.00% | 55.95% | 12.30% | NA |
| Japonica Intermediate | 241 | 10.80% | 10.40% | 69.29% | 9.54% | NA |
| VI/Aromatic | 96 | 70.80% | 2.10% | 26.04% | 1.04% | NA |
| Intermediate | 90 | 72.20% | 1.10% | 24.44% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109585484 | G -> A | LOC_Os11g17200.1 | synonymous_variant ; p.Ser67Ser; LOW | synonymous_codon | Average:6.757; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg1109585484 | G -> DEL | LOC_Os11g17200.1 | N | frameshift_variant | Average:6.757; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |