| Variant ID: vg0704650310 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4650310 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.05, others allele: 0.00, population size: 286. )
TGGCAATAATCTTGGCACACAACTCCTGGAATGTATCCTTTGGTTTCATCTCAACTTGAGCCATGTCGCCCTCGGCTTTGTTGGTTTTGATGGATGGTGA[C/T]
GGTGTTGCAATAGCAGCTGCGGTAGTTGAGGGTGTGGATGAGTTCATAGTGGCTGGAAACACATGTTCTGGTGCAGCAAGAGAACTCTCAACTGCTGGCC
GGCCAGCAGTTGAGAGTTCTCTTGCTGCACCAGAACATGTGTTTCCAGCCACTATGAACTCATCCACACCCTCAACTACCGCAGCTGCTATTGCAACACC[G/A]
TCACCATCCATCAAAACCAACAAAGCCGAGGGCGACATGGCTCAAGTTGAGATGAAACCAAAGGATACATTCCAGGAGTTGTGTGCCAAGATTATTGCCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.70% | 41.00% | 0.11% | 0.17% | NA |
| All Indica | 2759 | 97.40% | 2.30% | 0.11% | 0.25% | NA |
| All Japonica | 1512 | 0.40% | 99.50% | 0.07% | 0.07% | NA |
| Aus | 269 | 18.60% | 81.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.50% | 0.17% | 0.17% | NA |
| Indica II | 465 | 97.00% | 2.80% | 0.22% | 0.00% | NA |
| Indica III | 913 | 98.10% | 1.40% | 0.00% | 0.44% | NA |
| Indica Intermediate | 786 | 95.30% | 4.30% | 0.13% | 0.25% | NA |
| Temperate Japonica | 767 | 0.40% | 99.50% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.40% | 99.20% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 36.70% | 62.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0704650310 | C -> DEL | LOC_Os07g08940.1 | N | frameshift_variant | Average:54.211; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 | N | N | N | N |
| vg0704650310 | C -> T | LOC_Os07g08940.1 | synonymous_variant ; p.Pro82Pro; LOW | synonymous_codon | Average:54.211; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 | N | N | N | N |