| Variant ID: vg0410155005 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10155005 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 123. )
TTACACGATAGAAGTATTTAGTCCGAACACTCATTACATCACAACAGCATTTTATTTCCTAAATCGAAAGCATTGTTACACCATGGAATCGCCTGCTGCG[C/T]
GACGACGCCTTGGTCTTGCGCGCCTGCTTGTTGTTCCTTCACCAGGTGGTCGCCTACCATCACTTGCCTGTCCAGATGGACTAGCATCTGCGCCGCTTGG
CCAAGCGGCGCAGATGCTAGTCCATCTGGACAGGCAAGTGATGGTAGGCGACCACCTGGTGAAGGAACAACAAGCAGGCGCGCAAGACCAAGGCGTCGTC[G/A]
CGCAGCAGGCGATTCCATGGTGTAACAATGCTTTCGATTTAGGAAATAAAATGCTGTTGTGATGTAATGAGTGTTCGGACTAAATACTTCTATCGTGTAA
| 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 | 18.00% | 0.10% | 2.58% | 79.31% | NA |
| All Indica | 2759 | 1.20% | 0.00% | 0.91% | 97.90% | NA |
| All Japonica | 1512 | 53.00% | 0.40% | 6.28% | 40.28% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica I | 595 | 1.20% | 0.00% | 2.35% | 96.47% | NA |
| Indica II | 465 | 2.20% | 0.00% | 0.65% | 97.20% | NA |
| Indica III | 913 | 0.50% | 0.00% | 0.22% | 99.23% | NA |
| Indica Intermediate | 786 | 1.40% | 0.00% | 0.76% | 97.84% | NA |
| Temperate Japonica | 767 | 87.60% | 0.00% | 6.26% | 6.13% | NA |
| Tropical Japonica | 504 | 3.20% | 0.00% | 0.79% | 96.03% | NA |
| Japonica Intermediate | 241 | 47.30% | 2.50% | 17.84% | 32.37% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 15.60% | 1.10% | 2.22% | 81.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410155005 | C -> DEL | N | N | silent_mutation | Average:4.429; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0410155005 | C -> T | LOC_Os04g18400.1 | upstream_gene_variant ; 4052.0bp to feature; MODIFIER | silent_mutation | Average:4.429; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0410155005 | C -> T | LOC_Os04g18380.1 | downstream_gene_variant ; 4352.0bp to feature; MODIFIER | silent_mutation | Average:4.429; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0410155005 | C -> T | LOC_Os04g18390.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.429; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |