| Variant ID: vg0609018014 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9018014 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGACCTTGATAAATAATATTGTTTAGTTTTAGAATCGCGTTTACAAAATGGCTTTG[A/G]
GCAACTAATGTCTTTAAATGCTGTTTACTGCAATCCTAACCCTTTATAGTGTAACTCCTTTGTACTCCCTTGCATTTATTCTGCACTTGTGGGTGTGCCT
AGGCACACCCACAAGTGCAGAATAAATGCAAGGGAGTACAAAGGAGTTACACTATAAAGGGTTAGGATTGCAGTAAACAGCATTTAAAGACATTAGTTGC[T/C]
CAAAGCCATTTTGTAAACGCGATTCTAAAACTAAACAATATTATTTATCAAGGTCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.90% | 0.30% | 2.60% | 48.20% | NA |
| All Indica | 2759 | 59.20% | 0.10% | 1.49% | 39.22% | NA |
| All Japonica | 1512 | 40.90% | 0.60% | 1.85% | 56.68% | NA |
| Aus | 269 | 3.30% | 0.00% | 17.10% | 79.55% | NA |
| Indica I | 595 | 57.50% | 0.00% | 0.50% | 42.02% | NA |
| Indica II | 465 | 78.90% | 0.00% | 0.65% | 20.43% | NA |
| Indica III | 913 | 45.20% | 0.10% | 2.85% | 51.81% | NA |
| Indica Intermediate | 786 | 65.10% | 0.10% | 1.15% | 33.59% | NA |
| Temperate Japonica | 767 | 73.90% | 0.10% | 0.26% | 25.68% | NA |
| Tropical Japonica | 504 | 5.00% | 1.20% | 3.97% | 89.88% | NA |
| Japonica Intermediate | 241 | 10.80% | 0.80% | 2.49% | 85.89% | NA |
| VI/Aromatic | 96 | 3.10% | 1.00% | 5.21% | 90.62% | NA |
| Intermediate | 90 | 52.20% | 2.20% | 3.33% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609018014 | A -> G | LOC_Os06g15870.1 | upstream_gene_variant ; 3399.0bp to feature; MODIFIER | silent_mutation | Average:30.662; most accessible tissue: Zhenshan97 flag leaf, score: 77.473 | N | N | N | N |
| vg0609018014 | A -> G | LOC_Os06g15900.1 | upstream_gene_variant ; 3400.0bp to feature; MODIFIER | silent_mutation | Average:30.662; most accessible tissue: Zhenshan97 flag leaf, score: 77.473 | N | N | N | N |
| vg0609018014 | A -> G | LOC_Os06g15890.1 | downstream_gene_variant ; 1334.0bp to feature; MODIFIER | silent_mutation | Average:30.662; most accessible tissue: Zhenshan97 flag leaf, score: 77.473 | N | N | N | N |
| vg0609018014 | A -> G | LOC_Os06g15880.1 | intron_variant ; MODIFIER | silent_mutation | Average:30.662; most accessible tissue: Zhenshan97 flag leaf, score: 77.473 | N | N | N | N |
| vg0609018014 | A -> DEL | N | N | silent_mutation | Average:30.662; most accessible tissue: Zhenshan97 flag leaf, score: 77.473 | N | N | N | N |