| Variant ID: vg0609017980 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9017980 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCTGGGACCCAGGGTCGGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGACCTTGATAAATAATATTGT[T/A]
TAGTTTTAGAATCGCGTTTACAAAATGGCTTTGAGCAACTAATGTCTTTAAATGCTGTTTACTGCAATCCTAACCCTTTATAGTGTAACTCCTTTGTACT
AGTACAAAGGAGTTACACTATAAAGGGTTAGGATTGCAGTAAACAGCATTTAAAGACATTAGTTGCTCAAAGCCATTTTGTAAACGCGATTCTAAAACTA[A/T]
ACAATATTATTTATCAAGGTCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACCCGACCCTGGGTCCCAGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.10% | 0.20% | 2.92% | 48.73% | NA |
| All Indica | 2759 | 58.40% | 0.10% | 2.54% | 38.93% | NA |
| All Japonica | 1512 | 40.60% | 0.30% | 0.93% | 58.20% | NA |
| Aus | 269 | 1.50% | 0.00% | 16.36% | 82.16% | NA |
| Indica I | 595 | 57.10% | 0.00% | 0.50% | 42.35% | NA |
| Indica II | 465 | 78.50% | 0.20% | 0.86% | 20.43% | NA |
| Indica III | 913 | 43.50% | 0.20% | 6.13% | 50.16% | NA |
| Indica Intermediate | 786 | 64.80% | 0.10% | 0.89% | 34.22% | NA |
| Temperate Japonica | 767 | 73.30% | 0.00% | 0.52% | 26.21% | NA |
| Tropical Japonica | 504 | 4.60% | 0.60% | 1.59% | 93.25% | NA |
| Japonica Intermediate | 241 | 12.00% | 0.40% | 0.83% | 86.72% | NA |
| VI/Aromatic | 96 | 3.10% | 1.00% | 3.12% | 92.71% | NA |
| Intermediate | 90 | 46.70% | 2.20% | 7.78% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609017980 | T -> A | LOC_Os06g15870.1 | upstream_gene_variant ; 3365.0bp to feature; MODIFIER | silent_mutation | Average:30.859; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 | N | N | N | N |
| vg0609017980 | T -> A | LOC_Os06g15900.1 | upstream_gene_variant ; 3434.0bp to feature; MODIFIER | silent_mutation | Average:30.859; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 | N | N | N | N |
| vg0609017980 | T -> A | LOC_Os06g15890.1 | downstream_gene_variant ; 1368.0bp to feature; MODIFIER | silent_mutation | Average:30.859; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 | N | N | N | N |
| vg0609017980 | T -> A | LOC_Os06g15880.1 | intron_variant ; MODIFIER | silent_mutation | Average:30.859; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 | N | N | N | N |
| vg0609017980 | T -> DEL | N | N | silent_mutation | Average:30.859; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 | N | N | N | N |