| Variant ID: vg0708358679 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 8358679 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTCCGTCGCCTAGCAGTTCTTCTCCGGCTTGGTGAGCTTGCACTTGACCTTCTGGAACGCCACGGAGGTGGTGCCCGGCGGCGCGAGCTGCAGCTTGAGC[G/T]
GGCACGTCGCCTCGATCTTGCACTTGGTGAGCCTCGCCGTGTACCTCACCTCGCCGGCGATCGCCACCTCCACCTCGAACGTCCCCTTGGCGCTCTCCTT
AAGGAGAGCGCCAAGGGGACGTTCGAGGTGGAGGTGGCGATCGCCGGCGAGGTGAGGTACACGGCGAGGCTCACCAAGTGCAAGATCGAGGCGACGTGCC[C/A]
GCTCAAGCTGCAGCTCGCGCCGCCGGGCACCACCTCCGTGGCGTTCCAGAAGGTCAAGTGCAAGCTCACCAAGCCGGAGAAGAACTGCTAGGCGACGGAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.10% | 0.19% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.30% | 0.60% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.30% | 0.70% | 1.04% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0708358679 | G -> T | LOC_Os07g14660.1 | missense_variant ; p.Pro176Gln; MODERATE | N | Average:70.666; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |
| vg0708358679 | G -> T | LOC_Os07g14650.1 | downstream_gene_variant ; 3724.0bp to feature; MODIFIER | N | Average:70.666; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |
| vg0708358679 | G -> T | LOC_Os07g14670.1 | downstream_gene_variant ; 2386.0bp to feature; MODIFIER | N | Average:70.666; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |
| vg0708358679 | G -> T | LOC_Os07g14680.1 | downstream_gene_variant ; 4113.0bp to feature; MODIFIER | N | Average:70.666; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |
| vg0708358679 | G -> T | LOC_Os07g14650.2 | downstream_gene_variant ; 3724.0bp to feature; MODIFIER | N | Average:70.666; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |