| Variant ID: vg0710994234 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10994234 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GATGCTGCCGAGGATCTCGTCGGGGAGGACGCTGATCAGGTCGATGCCCCCCGCATCAGCATCGCCTCCCTCCGATCGTTCTTGGCAATCCGGTTCGTCG[T/A]
GTCTCCGTTTCTTGGCGACTGGAGCGGTCACCTCTTCCATGGCCGGCGGTAGGCCGTGGGCGGCGTGAGAGGTGGCGGTTGTGTTGATGAGAAATTGAGA
TCTCAATTTCTCATCAACACAACCGCCACCTCTCACGCCGCCCACGGCCTACCGCCGGCCATGGAAGAGGTGACCGCTCCAGTCGCCAAGAAACGGAGAC[A/T]
CGACGAACCGGATTGCCAAGAACGATCGGAGGGAGGCGATGCTGATGCGGGGGGCATCGACCTGATCAGCGTCCTCCCCGACGAGATCCTCGGCAGCATC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.90% | 0.10% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.20% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 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 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.50% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0710994234 | T -> A | LOC_Os07g18600.1 | missense_variant ; p.His14Leu; MODERATE | N | Average:72.643; most accessible tissue: Minghui63 flag leaf, score: 85.5 | N | N | N | N |
| vg0710994234 | T -> A | LOC_Os07g18580.1 | upstream_gene_variant ; 4702.0bp to feature; MODIFIER | N | Average:72.643; most accessible tissue: Minghui63 flag leaf, score: 85.5 | N | N | N | N |
| vg0710994234 | T -> A | LOC_Os07g18610.1 | upstream_gene_variant ; 3809.0bp to feature; MODIFIER | N | Average:72.643; most accessible tissue: Minghui63 flag leaf, score: 85.5 | N | N | N | N |
| vg0710994234 | T -> A | LOC_Os07g18590.1 | downstream_gene_variant ; 1793.0bp to feature; MODIFIER | N | Average:72.643; most accessible tissue: Minghui63 flag leaf, score: 85.5 | N | N | N | N |