| Variant ID: vg0609017968 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9017968 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGCTTGGGACGAGCTGGGACCCAGGGTCGGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGACCTTGAT[A/T]
AATAATATTGTTTAGTTTTAGAATCGCGTTTACAAAATGGCTTTGAGCAACTAATGTCTTTAAATGCTGTTTACTGCAATCCTAACCCTTTATAGTGTAA
TTACACTATAAAGGGTTAGGATTGCAGTAAACAGCATTTAAAGACATTAGTTGCTCAAAGCCATTTTGTAAACGCGATTCTAAAACTAAACAATATTATT[T/A]
ATCAAGGTCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACCCGACCCTGGGTCCCAGCTCGTCCCAAGCC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.80% | 0.10% | 9.37% | 39.65% | NA |
| All Indica | 2759 | 59.90% | 0.00% | 7.18% | 32.87% | NA |
| All Japonica | 1512 | 41.70% | 0.30% | 10.45% | 47.55% | NA |
| Aus | 269 | 23.40% | 0.00% | 14.87% | 61.71% | NA |
| Indica I | 595 | 57.30% | 0.00% | 1.68% | 41.01% | NA |
| Indica II | 465 | 79.80% | 0.00% | 6.88% | 13.33% | NA |
| Indica III | 913 | 46.40% | 0.10% | 10.95% | 42.50% | NA |
| Indica Intermediate | 786 | 65.80% | 0.00% | 7.12% | 27.10% | NA |
| Temperate Japonica | 767 | 73.40% | 0.00% | 1.96% | 24.64% | NA |
| Tropical Japonica | 504 | 6.30% | 0.80% | 19.25% | 73.61% | NA |
| Japonica Intermediate | 241 | 14.50% | 0.40% | 19.09% | 65.98% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 38.54% | 54.17% | NA |
| Intermediate | 90 | 54.40% | 1.10% | 11.11% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609017968 | A -> T | LOC_Os06g15870.1 | upstream_gene_variant ; 3353.0bp to feature; MODIFIER | silent_mutation | Average:32.188; most accessible tissue: Zhenshan97 flag leaf, score: 76.642 | N | N | N | N |
| vg0609017968 | A -> T | LOC_Os06g15900.1 | upstream_gene_variant ; 3446.0bp to feature; MODIFIER | silent_mutation | Average:32.188; most accessible tissue: Zhenshan97 flag leaf, score: 76.642 | N | N | N | N |
| vg0609017968 | A -> T | LOC_Os06g15890.1 | downstream_gene_variant ; 1380.0bp to feature; MODIFIER | silent_mutation | Average:32.188; most accessible tissue: Zhenshan97 flag leaf, score: 76.642 | N | N | N | N |
| vg0609017968 | A -> T | LOC_Os06g15880.1 | intron_variant ; MODIFIER | silent_mutation | Average:32.188; most accessible tissue: Zhenshan97 flag leaf, score: 76.642 | N | N | N | N |
| vg0609017968 | A -> DEL | N | N | silent_mutation | Average:32.188; most accessible tissue: Zhenshan97 flag leaf, score: 76.642 | N | N | N | N |