| Variant ID: vg0409854378 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 9854378 |
| Reference Allele: GC | Alternative Allele: G |
| Primary Allele: GC | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATTCCATCTCAGTCGGCAGCAACTGAAGAAACAAGGTGCTGTGACACCTGTAATGGGCCTATGGGCTTGTAACCTCATTTGGGACCCCGGCCCAGGTGGG[GC/G]
CCATGTGGGGTGCGCCCCAAGCTGGTGGAGCACGACCCTAGGCACCCCTAGGTCGTCCTCCCACCCCTATATATAGCTAGTTACCCCTTCAGGGTTTCTG
CAGAAACCCTGAAGGGGTAACTAGCTATATATAGGGGTGGGAGGACGACCTAGGGGTGCCTAGGGTCGTGCTCCACCAGCTTGGGGCGCACCCCACATGG[GC/C]
CCCACCTGGGCCGGGGTCCCAAATGAGGTTACAAGCCCATAGGCCCATTACAGGTGTCACAGCACCTTGTTTCTTCAGTTGCTGCCGACTGAGATGGAAT
| Populations | Population Size | Frequency of GC(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.80% | 0.10% | 4.38% | 65.72% | NA |
| All Indica | 2759 | 16.70% | 0.10% | 5.87% | 77.31% | NA |
| All Japonica | 1512 | 58.60% | 0.30% | 1.32% | 39.81% | NA |
| Aus | 269 | 11.20% | 0.00% | 4.09% | 84.76% | NA |
| Indica I | 595 | 13.80% | 0.30% | 5.04% | 80.84% | NA |
| Indica II | 465 | 13.50% | 0.00% | 3.23% | 83.23% | NA |
| Indica III | 913 | 21.40% | 0.00% | 7.78% | 70.87% | NA |
| Indica Intermediate | 786 | 15.50% | 0.00% | 5.85% | 78.63% | NA |
| Temperate Japonica | 767 | 92.80% | 0.30% | 0.26% | 6.65% | NA |
| Tropical Japonica | 504 | 4.20% | 0.20% | 0.79% | 94.84% | NA |
| Japonica Intermediate | 241 | 63.50% | 0.40% | 5.81% | 30.29% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 4.17% | 90.62% | NA |
| Intermediate | 90 | 26.70% | 0.00% | 11.11% | 62.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409854378 | GC -> DEL | N | N | silent_mutation | Average:5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0409854378 | GC -> G | LOC_Os04g17920.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0409854378 | GC -> G | LOC_Os04g17910.1 | upstream_gene_variant ; 3684.0bp to feature; MODIFIER | silent_mutation | Average:5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0409854378 | GC -> G | LOC_Os04g17930.1 | downstream_gene_variant ; 1758.0bp to feature; MODIFIER | silent_mutation | Average:5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |