| Variant ID: vg0609017960 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9017960 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 103. )
CCTGGGTTGGCTTGGGACGAGCTGGGACCCAGGGTCGGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACG[A/G]
CCTTGATAAATAATATTGTTTAGTTTTAGAATCGCGTTTACAAAATGGCTTTGAGCAACTAATGTCTTTAAATGCTGTTTACTGCAATCCTAACCCTTTA
TAAAGGGTTAGGATTGCAGTAAACAGCATTTAAAGACATTAGTTGCTCAAAGCCATTTTGTAAACGCGATTCTAAAACTAAACAATATTATTTATCAAGG[T/C]
CGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACCCGACCCTGGGTCCCAGCTCGTCCCAAGCCAACCCAGG
| 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 | 29.40% | 16.20% | 11.21% | 43.17% | NA |
| All Indica | 2759 | 48.70% | 5.00% | 11.71% | 34.54% | NA |
| All Japonica | 1512 | 0.90% | 39.20% | 6.55% | 53.44% | NA |
| Aus | 269 | 0.70% | 7.10% | 30.86% | 61.34% | NA |
| Indica I | 595 | 48.10% | 1.00% | 9.58% | 41.34% | NA |
| Indica II | 465 | 57.40% | 9.50% | 18.49% | 14.62% | NA |
| Indica III | 913 | 40.00% | 5.30% | 10.19% | 44.58% | NA |
| Indica Intermediate | 786 | 54.30% | 5.10% | 11.07% | 29.52% | NA |
| Temperate Japonica | 767 | 0.70% | 71.70% | 1.17% | 26.47% | NA |
| Tropical Japonica | 504 | 0.80% | 3.60% | 10.52% | 85.12% | NA |
| Japonica Intermediate | 241 | 1.70% | 10.00% | 15.35% | 73.03% | NA |
| VI/Aromatic | 96 | 0.00% | 4.20% | 15.62% | 80.21% | NA |
| Intermediate | 90 | 32.20% | 15.60% | 11.11% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609017960 | A -> G | LOC_Os06g15870.1 | upstream_gene_variant ; 3345.0bp to feature; MODIFIER | silent_mutation | Average:32.13; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |
| vg0609017960 | A -> G | LOC_Os06g15900.1 | upstream_gene_variant ; 3454.0bp to feature; MODIFIER | silent_mutation | Average:32.13; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |
| vg0609017960 | A -> G | LOC_Os06g15890.1 | downstream_gene_variant ; 1388.0bp to feature; MODIFIER | silent_mutation | Average:32.13; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |
| vg0609017960 | A -> G | LOC_Os06g15880.1 | intron_variant ; MODIFIER | silent_mutation | Average:32.13; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |
| vg0609017960 | A -> DEL | N | N | silent_mutation | Average:32.13; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |