| Variant ID: vg0302880239 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 2880239 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTGCGGCCTCCGAGGATGAAAACCAAGCGGCAGCTGGTGGCGCCGCCGGCGATGAGGCGGCGGCGGAGGAGGAGGGGACCAAGTCCAACAAGAAGAAGGC[C/T]
GAGCGGGTGACCGCAGAAGTACCTGCCGACGAGGCGGCGCCGGCGGCAAAGAAGCCGAGGGCGATGGGCGGACAATCGTTCAGCATGGCCGGCGCCGGCG
CGCCGGCGCCGGCCATGCTGAACGATTGTCCGCCCATCGCCCTCGGCTTCTTTGCCGCCGGCGCCGCCTCGTCGGCAGGTACTTCTGCGGTCACCCGCTC[G/A]
GCCTTCTTCTTGTTGGACTTGGTCCCCTCCTCCTCCGCCGCCGCCTCATCGCCGGCGGCGCCACCAGCTGCCGCTTGGTTTTCATCCTCGGAGGCCGCAG
| 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 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0302880239 | C -> T | LOC_Os03g05770.1 | synonymous_variant ; p.Ala428Ala; LOW | N | Average:74.942; most accessible tissue: Minghui63 panicle, score: 87.951 | N | N | N | N |
| vg0302880239 | C -> T | LOC_Os03g05760.1 | downstream_gene_variant ; 4809.0bp to feature; MODIFIER | N | Average:74.942; most accessible tissue: Minghui63 panicle, score: 87.951 | N | N | N | N |
| vg0302880239 | C -> T | LOC_Os03g05780.1 | downstream_gene_variant ; 2766.0bp to feature; MODIFIER | N | Average:74.942; most accessible tissue: Minghui63 panicle, score: 87.951 | N | N | N | N |