| Variant ID: vg0315011440 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 15011440 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACAAGGTGTGGCTGCTGCAGACGCGCGACGCCGTCTTCGACGCCGAGGACGCCCTCGATCATTTCTATCTCCGCGTCGATATGTCCAGGTATATATAGCT[G/A]
CTACTAGATACTCCCTCTATTTTTTAATAGACGACGCCGTTGACTTTTTCTTCCATATTTGACTATTCGTCTTATTCAAAAAATTTTATGTAAATATATA
TATATATTTACATAAAATTTTTTGAATAAGACGAATAGTCAAATATGGAAGAAAAAGTCAACGGCGTCGTCTATTAAAAAATAGAGGGAGTATCTAGTAG[C/T]
AGCTATATATACCTGGACATATCGACGCGGAGATAGAAATGATCGAGGGCGTCCTCGGCGTCGAAGACGGCGTCGCGCGTCTGCAGCAGCCACACCTTGT
| 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 | 99.10% | 0.10% | 0.08% | 0.74% | NA |
| All Indica | 2759 | 99.80% | 0.00% | 0.04% | 0.11% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 87.00% | 0.00% | 1.12% | 11.90% | 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 | 99.60% | 0.00% | 0.11% | 0.33% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 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 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0315011440 | G -> A | LOC_Os03g26240.1 | upstream_gene_variant ; 1987.0bp to feature; MODIFIER | silent_mutation | Average:62.408; most accessible tissue: Minghui63 root, score: 79.068 | N | N | N | N |
| vg0315011440 | G -> A | LOC_Os03g26260.1 | upstream_gene_variant ; 4366.0bp to feature; MODIFIER | silent_mutation | Average:62.408; most accessible tissue: Minghui63 root, score: 79.068 | N | N | N | N |
| vg0315011440 | G -> A | LOC_Os03g26229.1 | downstream_gene_variant ; 3180.0bp to feature; MODIFIER | silent_mutation | Average:62.408; most accessible tissue: Minghui63 root, score: 79.068 | N | N | N | N |
| vg0315011440 | G -> A | LOC_Os03g26250.1 | intron_variant ; MODIFIER | silent_mutation | Average:62.408; most accessible tissue: Minghui63 root, score: 79.068 | N | N | N | N |
| vg0315011440 | G -> DEL | N | N | silent_mutation | Average:62.408; most accessible tissue: Minghui63 root, score: 79.068 | N | N | N | N |