| Variant ID: vg0500376103 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 376103 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TAATTTACTTTATCAGATATTGATATCACATTTAACTTAATATAACATATATCCCTTTCTTCTATGCCACAAAAGACAAAGCCCAAACCAGATGAACGCA[G/A]
GCGCTAGTTATCGAGAGCATTTATAAAGTGAATGAGAATTCTCTCTATTCATATAATTGTCTTCCACTGGCACTAAGCAAGTGTATATTCAGAGACTTGC
GCAAGTCTCTGAATATACACTTGCTTAGTGCCAGTGGAAGACAATTATATGAATAGAGAGAATTCTCATTCACTTTATAAATGCTCTCGATAACTAGCGC[C/T]
TGCGTTCATCTGGTTTGGGCTTTGTCTTTTGTGGCATAGAAGAAAGGGATATATGTTATATTAAGTTAAATGTGATATCAATATCTGATAAAGTAAATTA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.90% | 0.10% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.50% | 0.30% | 0.13% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.10% | 0.70% | 0.26% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0500376103 | G -> A | LOC_Os05g01635.1 | 3_prime_UTR_variant ; 367.0bp to feature; MODIFIER | N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0500376103 | G -> A | LOC_Os05g01630.1 | upstream_gene_variant ; 420.0bp to feature; MODIFIER | N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0500376103 | G -> A | LOC_Os05g01630.2 | upstream_gene_variant ; 420.0bp to feature; MODIFIER | N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0500376103 | G -> A | LOC_Os05g01630.3 | upstream_gene_variant ; 420.0bp to feature; MODIFIER | N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |