| Variant ID: vg0221476344 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 21476344 |
| Reference Allele: GCTGTAGTTCGTTGAGTAATGA | Alternative Allele: G |
| Primary Allele: GCTGTAGTTCGTTGAGTAAT GA | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTACTGTTGCTCTTTATCTCGTGTTTGCTTTAAATTTGGGAGTGTTTTTTTAAGTTTACTTTGAAGTACACTTGCTTCGAGTGATTTGGTGTAATAATCG[GCTGTAGTTCGTTGAGTAATGA/G]
CTGGGATGGTTTTCTATTCCATTATGTAAGAAAAACATAAGGTAGTAGTGAAATGGAAAAGACTTATTACCGTGAAGAATGTTGTGTAAAGAACCCATGG
CCATGGGTTCTTTACACAACATTCTTCACGGTAATAAGTCTTTTCCATTTCACTACTACCTTATGTTTTTCTTACATAATGGAATAGAAAACCATCCCAG[TCATTACTCAACGAACTACAGC/C]
CGATTATTACACCAAATCACTCGAAGCAAGTGTACTTCAAAGTAAACTTAAAAAAACACTCCCAAATTTAAAGCAAACACGAGATAAAGAGCAACAGTAA
| Populations | Population Size | Frequency of GCTGTAGTTCGTTGAGTAAT GA(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.90% | 4.10% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 97.70% | 2.20% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 51.70% | 48.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.50% | 4.30% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221476344 | GCTGTAGTTCGTTGAGTAATGA -> G | LOC_Os02g35750.1 | downstream_gene_variant ; 2523.0bp to feature; MODIFIER | silent_mutation | Average:66.018; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 | N | N | N | N |
| vg0221476344 | GCTGTAGTTCGTTGAGTAATGA -> G | LOC_Os02g35750.2 | downstream_gene_variant ; 877.0bp to feature; MODIFIER | silent_mutation | Average:66.018; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 | N | N | N | N |
| vg0221476344 | GCTGTAGTTCGTTGAGTAATGA -> G | LOC_Os02g35750.3 | downstream_gene_variant ; 712.0bp to feature; MODIFIER | silent_mutation | Average:66.018; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 | N | N | N | N |
| vg0221476344 | GCTGTAGTTCGTTGAGTAATGA -> G | LOC_Os02g35760.1 | intron_variant ; MODIFIER | silent_mutation | Average:66.018; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 | N | N | N | N |
| vg0221476344 | GCTGTAGTTCGTTGAGTAATGA -> G | LOC_Os02g35760.2 | intron_variant ; MODIFIER | silent_mutation | Average:66.018; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 | N | N | N | N |