| Variant ID: vg0609017914 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9017914 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTTAATTCTTAAAACCTGCTTAACGACTAAAATGTGGAATGGTTGGCCTGGGTTGGCTTGGGACGAGCTGGGACCCAGGGTCGGGTTGCCAGTTCGGTCT[G/A]
AATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGACCTTGATAAATAATATTGTTTAGTTTTAGAATCGCGTTTACAAAATGGCTTTGA
TCAAAGCCATTTTGTAAACGCGATTCTAAAACTAAACAATATTATTTATCAAGGTCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATT[C/T]
AGACCGAACTGGCAACCCGACCCTGGGTCCCAGCTCGTCCCAAGCCAACCCAGGCCAACCATTCCACATTTTAGTCGTTAAGCAGGTTTTAAGAATTAAA
| 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 | 49.60% | 0.50% | 7.66% | 42.26% | NA |
| All Indica | 2759 | 61.10% | 0.10% | 7.25% | 31.50% | NA |
| All Japonica | 1512 | 39.70% | 0.90% | 2.58% | 56.81% | NA |
| Aus | 269 | 3.30% | 2.20% | 36.06% | 58.36% | NA |
| Indica I | 595 | 57.60% | 0.00% | 4.03% | 38.32% | NA |
| Indica II | 465 | 81.10% | 0.00% | 5.16% | 13.76% | NA |
| Indica III | 913 | 48.00% | 0.20% | 11.06% | 40.74% | NA |
| Indica Intermediate | 786 | 67.30% | 0.10% | 6.49% | 26.08% | NA |
| Temperate Japonica | 767 | 72.60% | 0.10% | 0.65% | 26.60% | NA |
| Tropical Japonica | 504 | 3.80% | 2.40% | 5.56% | 88.29% | NA |
| Japonica Intermediate | 241 | 10.40% | 0.00% | 2.49% | 87.14% | NA |
| VI/Aromatic | 96 | 1.00% | 1.00% | 16.67% | 81.25% | NA |
| Intermediate | 90 | 50.00% | 1.10% | 11.11% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609017914 | G -> A | LOC_Os06g15870.1 | upstream_gene_variant ; 3299.0bp to feature; MODIFIER | silent_mutation | Average:31.333; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |
| vg0609017914 | G -> A | LOC_Os06g15900.1 | upstream_gene_variant ; 3500.0bp to feature; MODIFIER | silent_mutation | Average:31.333; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |
| vg0609017914 | G -> A | LOC_Os06g15890.1 | downstream_gene_variant ; 1434.0bp to feature; MODIFIER | silent_mutation | Average:31.333; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |
| vg0609017914 | G -> A | LOC_Os06g15880.1 | intron_variant ; MODIFIER | silent_mutation | Average:31.333; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |
| vg0609017914 | G -> DEL | N | N | silent_mutation | Average:31.333; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |