| Variant ID: vg0510478743 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 10478743 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTGCTCGGCTCGCCCATAACCGAGGGCGCGGCTATTCGAATAGATTATACTCTGATCAGAGGTGTACAACTTTACCCACAAGACACATCTTCCTCACGTG[C/T]
AACCACGTGCCACATACCACCACGGTATACAGACGGAAGACGTGACATAGTTTCCAACCCATCCTAGCCATAGACAAGAGTACCGACCCAATCCCACCTA
TAGGTGGGATTGGGTCGGTACTCTTGTCTATGGCTAGGATGGGTTGGAAACTATGTCACGTCTTCCGTCTGTATACCGTGGTGGTATGTGGCACGTGGTT[G/A]
CACGTGAGGAAGATGTGTCTTGTGGGTAAAGTTGTACACCTCTGATCAGAGTATAATCTATTCGAATAGCCGCGCCCTCGGTTATGGGCGAGCCGAGCAA
| 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 | 90.30% | 5.90% | 3.81% | 0.00% | NA |
| All Indica | 2759 | 90.40% | 5.50% | 4.13% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.10% | 0.13% | 0.00% | NA |
| Aus | 269 | 31.60% | 46.50% | 21.93% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.30% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.40% | 0.22% | 0.00% | NA |
| Indica III | 913 | 79.30% | 12.70% | 8.00% | 0.00% | NA |
| Indica Intermediate | 786 | 91.10% | 4.10% | 4.83% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 2.20% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0510478743 | C -> T | LOC_Os05g18210.1 | downstream_gene_variant ; 1576.0bp to feature; MODIFIER | silent_mutation | Average:23.422; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | N | N | N | N |
| vg0510478743 | C -> T | LOC_Os05g18230.1 | downstream_gene_variant ; 2405.0bp to feature; MODIFIER | silent_mutation | Average:23.422; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | N | N | N | N |
| vg0510478743 | C -> T | LOC_Os05g18220.1 | intron_variant ; MODIFIER | silent_mutation | Average:23.422; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | N | N | N | N |