| Variant ID: vg0609018352 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9018352 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTTTCTCGTTTGTCTCTGTGTGTGCCGGGCCTCCGCTGCCCATGTAATAAATTAACTATTTACGCTTCCGCTTGTTAAACTCTGAATTGTATCAACTTTT[G/A]
GTGTACCTTGCCTCCTGGGACAAGGATTAATGCACGCACGTAAGGAACGCCCGTTGGGTTATTTCCGGTTGTGACAACTTGACTCTTGGCTAATCAACCC
GGGTTGATTAGCCAAGAGTCAAGTTGTCACAACCGGAAATAACCCAACGGGCGTTCCTTACGTGCGTGCATTAATCCTTGTCCCAGGAGGCAAGGTACAC[C/T]
AAAAGTTGATACAATTCAGAGTTTAACAAGCGGAAGCGTAAATAGTTAATTTATTACATGGGCAGCGGAGGCCCGGCACACACAGAGACAAACGAGAAAC
| 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 | 49.00% | 0.20% | 10.01% | 40.82% | NA |
| All Indica | 2759 | 58.80% | 0.00% | 7.07% | 34.14% | NA |
| All Japonica | 1512 | 37.20% | 0.60% | 13.36% | 48.81% | NA |
| Aus | 269 | 28.30% | 0.00% | 11.15% | 60.59% | NA |
| Indica I | 595 | 57.30% | 0.00% | 1.68% | 41.01% | NA |
| Indica II | 465 | 78.70% | 0.00% | 7.96% | 13.33% | NA |
| Indica III | 913 | 43.80% | 0.00% | 10.73% | 45.45% | NA |
| Indica Intermediate | 786 | 65.50% | 0.00% | 6.36% | 28.12% | NA |
| Temperate Japonica | 767 | 67.50% | 1.20% | 6.39% | 24.90% | NA |
| Tropical Japonica | 504 | 3.00% | 0.00% | 20.44% | 76.59% | NA |
| Japonica Intermediate | 241 | 12.40% | 0.00% | 20.75% | 66.80% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 34.38% | 58.33% | NA |
| Intermediate | 90 | 52.20% | 0.00% | 14.44% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609018352 | G -> A | LOC_Os06g15870.1 | upstream_gene_variant ; 3737.0bp to feature; MODIFIER | silent_mutation | Average:31.82; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | N | N | N | N |
| vg0609018352 | G -> A | LOC_Os06g15900.1 | upstream_gene_variant ; 3062.0bp to feature; MODIFIER | silent_mutation | Average:31.82; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | N | N | N | N |
| vg0609018352 | G -> A | LOC_Os06g15890.1 | downstream_gene_variant ; 996.0bp to feature; MODIFIER | silent_mutation | Average:31.82; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | N | N | N | N |
| vg0609018352 | G -> A | LOC_Os06g15880.1 | intron_variant ; MODIFIER | silent_mutation | Average:31.82; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | N | N | N | N |
| vg0609018352 | G -> DEL | N | N | silent_mutation | Average:31.82; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | N | N | N | N |