| Variant ID: vg1009464437 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 9464437 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.10, others allele: 0.00, population size: 80. )
GCCTCATCGGCTGCAGCATCATCGGCTACAGGAACCTGATTCTTAACACGCCACTCCTGTCTTGGCCTTGGTTTCCTCAGCCGATGGTTAATTTCTTGTT[T/C]
AACCTCCTGAAGACGCTCCCTGTTCCTCAATCTCTGGACCCTTCTTTTCTGATTCTTCGTGAAAATACCAGAAGGACACCATTGATTCTTCCTGATTGCC
GGCAATCAGGAAGAATCAATGGTGTCCTTCTGGTATTTTCACGAAGAATCAGAAAAGAAGGGTCCAGAGATTGAGGAACAGGGAGCGTCTTCAGGAGGTT[A/G]
AACAAGAAATTAACCATCGGCTGAGGAAACCAAGGCCAAGACAGGAGTGGCGTGTTAAGAATCAGGTTCCTGTAGCCGATGATGCTGCAGCCGATGAGGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 44.40% | 11.80% | 0.28% | 43.55% | NA |
| All Indica | 2759 | 36.80% | 1.20% | 0.33% | 61.62% | NA |
| All Japonica | 1512 | 45.00% | 33.70% | 0.13% | 21.10% | NA |
| Aus | 269 | 97.40% | 0.40% | 0.00% | 2.23% | NA |
| Indica I | 595 | 72.60% | 0.80% | 0.34% | 26.22% | NA |
| Indica II | 465 | 18.50% | 1.70% | 0.00% | 79.78% | NA |
| Indica III | 913 | 20.20% | 0.30% | 0.22% | 79.30% | NA |
| Indica Intermediate | 786 | 39.90% | 2.30% | 0.64% | 57.12% | NA |
| Temperate Japonica | 767 | 38.20% | 50.50% | 0.00% | 11.34% | NA |
| Tropical Japonica | 504 | 60.50% | 7.70% | 0.20% | 31.55% | NA |
| Japonica Intermediate | 241 | 34.40% | 34.90% | 0.41% | 30.29% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 53.30% | 15.60% | 2.22% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1009464437 | T -> C | LOC_Os10g18650.1 | upstream_gene_variant ; 4652.0bp to feature; MODIFIER | silent_mutation | Average:11.99; most accessible tissue: Zhenshan97 flag leaf, score: 21.748 | N | N | N | N |
| vg1009464437 | T -> C | LOC_Os10g18660.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.99; most accessible tissue: Zhenshan97 flag leaf, score: 21.748 | N | N | N | N |
| vg1009464437 | T -> DEL | N | N | silent_mutation | Average:11.99; most accessible tissue: Zhenshan97 flag leaf, score: 21.748 | N | N | N | N |