| Variant ID: vg1101999320 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1999320 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 254. )
GCCCGGTGTGCCTTCAGGGCTTCGAGGAGGGCGACAAGCTTAGGAAGATGCCGTGCGCTGATTCGCACTGCTTCCATGAGCAGTGCATATTCAGCTGGCT[T/C]
CTGATTAACCGCCATTGCCCGCTCTGCCGCTTCCCGTTGCCTGCTGAGACGGAGGAGGATGAAGAGGTGGTCCAGGCAGAGAACGACGACGACGACGATG
CATCGTCGTCGTCGTCGTTCTCTGCCTGGACCACCTCTTCATCCTCCTCCGTCTCAGCAGGCAACGGGAAGCGGCAGAGCGGGCAATGGCGGTTAATCAG[A/G]
AGCCAGCTGAATATGCACTGCTCATGGAAGCAGTGCGAATCAGCGCACGGCATCTTCCTAAGCTTGTCGCCCTCCTCGAAGCCCTGAAGGCACACCGGGC
| 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 | 64.50% | 35.50% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 95.30% | 4.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 3.10% | 96.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 92.90% | 7.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 2.60% | 97.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 2.80% | 97.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 5.40% | 94.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 60.40% | 39.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 48.90% | 50.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101999320 | T -> C | LOC_Os11g04690.1 | synonymous_variant ; p.Leu177Leu; LOW | synonymous_codon | Average:66.966; most accessible tissue: Minghui63 root, score: 76.119 | N | N | N | N |