| Variant ID: vg1007671345 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7671345 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATCGGCATCGGACATTTAATTGACACAGAACTCAATAGCCTCCTCGGTCGTGTAACCTTCAATGATGCTCCCCTCGGGTTTAGCTCTGTTACGAACGTAC[A/G]
ACTTCAGAACTCCCATGTACCTTTCAAACGGCCACATTTCCCTTAGAAAAGCCGGGCCACATAGTTTTGTTTGCTTCACCAGATGAACAGGGAGATGAAC
GTTCATCTCCCTGTTCATCTGGTGAAGCAAACAAAACTATGTGGCCCGGCTTTTCTAAGGGAAATGTGGCCGTTTGAAAGGTACATGGGAGTTCTGAAGT[T/C]
GTACGTTCGTAACAGAGCTAAACCCGAGGGGAGCATCATTGAAGGTTACACGACCGAGGAGGCTATTGAGTTCTGTGTCAATTAAATGTCCGATGCCGAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.50% | 0.40% | 15.30% | 38.76% | NA |
| All Indica | 2759 | 46.00% | 0.70% | 7.68% | 45.63% | NA |
| All Japonica | 1512 | 53.90% | 0.00% | 17.00% | 29.10% | NA |
| Aus | 269 | 2.20% | 0.00% | 69.52% | 28.25% | NA |
| Indica I | 595 | 29.10% | 0.00% | 4.20% | 66.72% | NA |
| Indica II | 465 | 62.40% | 0.00% | 4.73% | 32.90% | NA |
| Indica III | 913 | 48.30% | 1.80% | 9.97% | 39.98% | NA |
| Indica Intermediate | 786 | 46.30% | 0.50% | 9.41% | 43.77% | NA |
| Temperate Japonica | 767 | 69.10% | 0.00% | 23.47% | 7.43% | NA |
| Tropical Japonica | 504 | 21.40% | 0.00% | 12.30% | 66.27% | NA |
| Japonica Intermediate | 241 | 73.40% | 0.00% | 6.22% | 20.33% | NA |
| VI/Aromatic | 96 | 22.90% | 0.00% | 47.92% | 29.17% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 23.33% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007671345 | A -> G | LOC_Os10g14120.1 | upstream_gene_variant ; 3768.0bp to feature; MODIFIER | silent_mutation | Average:7.481; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1007671345 | A -> G | LOC_Os10g14140.1 | downstream_gene_variant ; 1667.0bp to feature; MODIFIER | silent_mutation | Average:7.481; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1007671345 | A -> G | LOC_Os10g14150.1 | downstream_gene_variant ; 3930.0bp to feature; MODIFIER | silent_mutation | Average:7.481; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1007671345 | A -> G | LOC_Os10g14130.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.481; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1007671345 | A -> DEL | N | N | silent_mutation | Average:7.481; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |