| Variant ID: vg1007671341 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7671341 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TAGGATCGGCATCGGACATTTAATTGACACAGAACTCAATAGCCTCCTCGGTCGTGTAACCTTCAATGATGCTCCCCTCGGGTTTAGCTCTGTTACGAAC[G/A]
TACAACTTCAGAACTCCCATGTACCTTTCAAACGGCCACATTTCCCTTAGAAAAGCCGGGCCACATAGTTTTGTTTGCTTCACCAGATGAACAGGGAGAT
ATCTCCCTGTTCATCTGGTGAAGCAAACAAAACTATGTGGCCCGGCTTTTCTAAGGGAAATGTGGCCGTTTGAAAGGTACATGGGAGTTCTGAAGTTGTA[C/T]
GTTCGTAACAGAGCTAAACCCGAGGGGAGCATCATTGAAGGTTACACGACCGAGGAGGCTATTGAGTTCTGTGTCAATTAAATGTCCGATGCCGATCCTA
| 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 | 49.50% | 0.40% | 14.30% | 35.74% | NA |
| All Indica | 2759 | 49.70% | 0.70% | 8.30% | 41.25% | NA |
| All Japonica | 1512 | 54.40% | 0.00% | 17.00% | 28.57% | NA |
| Aus | 269 | 20.80% | 0.00% | 53.16% | 26.02% | NA |
| Indica I | 595 | 38.00% | 0.00% | 4.37% | 57.65% | NA |
| Indica II | 465 | 60.60% | 0.00% | 8.39% | 30.97% | NA |
| Indica III | 913 | 50.80% | 1.80% | 9.75% | 37.68% | NA |
| Indica Intermediate | 786 | 50.90% | 0.50% | 9.54% | 39.06% | NA |
| Temperate Japonica | 767 | 69.00% | 0.00% | 23.47% | 7.56% | NA |
| Tropical Japonica | 504 | 23.20% | 0.00% | 11.90% | 64.88% | NA |
| Japonica Intermediate | 241 | 73.40% | 0.00% | 7.05% | 19.50% | NA |
| VI/Aromatic | 96 | 44.80% | 0.00% | 28.12% | 27.08% | NA |
| Intermediate | 90 | 52.20% | 0.00% | 22.22% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007671341 | G -> A | LOC_Os10g14120.1 | upstream_gene_variant ; 3764.0bp to feature; MODIFIER | silent_mutation | Average:7.481; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1007671341 | G -> A | LOC_Os10g14140.1 | downstream_gene_variant ; 1671.0bp to feature; MODIFIER | silent_mutation | Average:7.481; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1007671341 | G -> A | LOC_Os10g14150.1 | downstream_gene_variant ; 3934.0bp to feature; MODIFIER | silent_mutation | Average:7.481; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1007671341 | G -> A | LOC_Os10g14130.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.481; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1007671341 | G -> DEL | N | N | silent_mutation | Average:7.481; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |