| Variant ID: vg1114173475 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 14173475 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGTTGATGACACAACTGCTACCAGTTGTAATAAGGGGTATCCTTCCAGACAATGTCCGGACAACAATAACAAAGCTATGTGCATTCATGAACGCAATTTC[G/A]
CAGAAGGTCATCGATCCGGATAGATTAGAAGCCCTTCAGAATGAAGTGGTGCAATGTCTCGTCAGTTTTGAGTTGATATTTCCACCTTCATTTTTCAATA
TATTGAAAAATGAAGGTGGAAATATCAACTCAAAACTGACGAGACATTGCACCACTTCATTCTGAAGGGCTTCTAATCTATCCGGATCGATGACCTTCTG[C/T]
GAAATTGCGTTCATGAATGCACATAGCTTTGTTATTGTTGTCCGGACATTGTCTGGAAGGATACCCCTTATTACAACTGGTAGCAGTTGTGTCATCAACA
| 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 | 3.20% | 0.50% | 5.42% | 90.92% | NA |
| All Indica | 2759 | 4.90% | 0.30% | 2.79% | 91.99% | NA |
| All Japonica | 1512 | 0.60% | 0.10% | 9.92% | 89.35% | NA |
| Aus | 269 | 1.90% | 2.20% | 3.72% | 92.19% | NA |
| Indica I | 595 | 3.40% | 0.00% | 0.34% | 96.30% | NA |
| Indica II | 465 | 8.20% | 0.20% | 4.09% | 87.53% | NA |
| Indica III | 913 | 4.60% | 0.40% | 3.07% | 91.89% | NA |
| Indica Intermediate | 786 | 4.50% | 0.50% | 3.56% | 91.48% | NA |
| Temperate Japonica | 767 | 0.80% | 0.00% | 5.74% | 93.48% | NA |
| Tropical Japonica | 504 | 0.40% | 0.40% | 16.07% | 83.13% | NA |
| Japonica Intermediate | 241 | 0.40% | 0.00% | 10.37% | 89.21% | NA |
| VI/Aromatic | 96 | 0.00% | 5.20% | 18.75% | 76.04% | NA |
| Intermediate | 90 | 2.20% | 0.00% | 1.11% | 96.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114173475 | G -> A | LOC_Os11g24860.1 | synonymous_variant ; p.Ser702Ser; LOW | synonymous_codon | Average:7.227; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg1114173475 | G -> DEL | LOC_Os11g24860.1 | N | frameshift_variant | Average:7.227; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |