| Variant ID: vg1114173466 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 14173466 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 372. )
ACTGTCACGTGTTGATGACACAACTGCTACCAGTTGTAATAAGGGGTATCCTTCCAGACAATGTCCGGACAACAATAACAAAGCTATGTGCATTCATGAA[C/T]
GCAATTTCGCAGAAGGTCATCGATCCGGATAGATTAGAAGCCCTTCAGAATGAAGTGGTGCAATGTCTCGTCAGTTTTGAGTTGATATTTCCACCTTCAT
ATGAAGGTGGAAATATCAACTCAAAACTGACGAGACATTGCACCACTTCATTCTGAAGGGCTTCTAATCTATCCGGATCGATGACCTTCTGCGAAATTGC[G/A]
TTCATGAATGCACATAGCTTTGTTATTGTTGTCCGGACATTGTCTGGAAGGATACCCCTTATTACAACTGGTAGCAGTTGTGTCATCAACACGTGACAGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 6.70% | 0.10% | 6.96% | 86.23% | NA |
| All Indica | 2759 | 7.20% | 0.20% | 5.26% | 87.39% | NA |
| All Japonica | 1512 | 2.90% | 0.10% | 9.79% | 87.24% | NA |
| Aus | 269 | 20.10% | 0.00% | 5.58% | 74.35% | NA |
| Indica I | 595 | 4.20% | 0.20% | 4.20% | 91.43% | NA |
| Indica II | 465 | 11.20% | 0.00% | 3.44% | 85.38% | NA |
| Indica III | 913 | 7.00% | 0.30% | 6.35% | 86.31% | NA |
| Indica Intermediate | 786 | 7.30% | 0.10% | 5.85% | 86.77% | NA |
| Temperate Japonica | 767 | 1.00% | 0.00% | 8.08% | 90.87% | NA |
| Tropical Japonica | 504 | 6.30% | 0.20% | 11.90% | 81.55% | NA |
| Japonica Intermediate | 241 | 1.70% | 0.00% | 10.79% | 87.55% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 18.75% | 64.58% | NA |
| Intermediate | 90 | 4.40% | 0.00% | 3.33% | 92.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114173466 | C -> T | LOC_Os11g24860.1 | synonymous_variant ; p.Asn699Asn; LOW | synonymous_codon | Average:7.227; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg1114173466 | C -> DEL | LOC_Os11g24860.1 | N | frameshift_variant | Average:7.227; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |