| Variant ID: vg0510478446 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 10478446 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAATGCAAGGGAGTACAAAGGAGTTATACTATAAAGGGTTAGGGTTTGCAGTAAACAGCATTTAAAGATATTTAGTTGCTCAGAGCTATTTTGTAAACAC[G/A]
ATTCTAGAACTGTACAATATTATTTATCAAGGCCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACCCGAC
GTCGGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGGCCTTGATAAATAATATTGTACAGTTCTAGAAT[C/T]
GTGTTTACAAAATAGCTCTGAGCAACTAAATATCTTTAAATGCTGTTTACTGCAAACCCTAACCCTTTATAGTATAACTCCTTTGTACTCCCTTGCATTT
| 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 | 94.40% | 0.90% | 4.68% | 0.00% | NA |
| All Indica | 2759 | 94.90% | 0.10% | 5.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 56.50% | 14.10% | 29.37% | 0.00% | NA |
| Indica I | 595 | 93.90% | 0.00% | 6.05% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.00% | 0.65% | 0.00% | NA |
| Indica III | 913 | 92.10% | 0.30% | 7.56% | 0.00% | NA |
| Indica Intermediate | 786 | 96.10% | 0.10% | 3.82% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 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% | 0.00% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0510478446 | G -> A | LOC_Os05g18210.1 | downstream_gene_variant ; 1279.0bp to feature; MODIFIER | silent_mutation | Average:19.275; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 | N | N | N | N |
| vg0510478446 | G -> A | LOC_Os05g18230.1 | downstream_gene_variant ; 2702.0bp to feature; MODIFIER | silent_mutation | Average:19.275; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 | N | N | N | N |
| vg0510478446 | G -> A | LOC_Os05g18220.1 | intron_variant ; MODIFIER | silent_mutation | Average:19.275; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 | N | N | N | N |