| Variant ID: vg0521976073 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 21976073 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GAAAAGTTCAGTGTGTGCTATATTGCAGAGGAGTTCAGTATGTTGCACAGAAAATTCAGAACATACTATATGCTGTCGTATAACAAAGTTCAGTACATAG[C/T]
CTCCCATAGAAAAATTCAGTATATATGTGAAAAATTCAGTAAATACTAGTGCGTATCAAAGTTCAGACTACGAATCACTATGGAAAGATTTAGTATACGT
ACGTATACTAAATCTTTCCATAGTGATTCGTAGTCTGAACTTTGATACGCACTAGTATTTACTGAATTTTTCACATATATACTGAATTTTTCTATGGGAG[G/A]
CTATGTACTGAACTTTGTTATACGACAGCATATAGTATGTTCTGAATTTTCTGTGCAACATACTGAACTCCTCTGCAATATAGCACACACTGAACTTTTC
| 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 | 59.50% | 13.40% | 26.96% | 0.19% | NA |
| All Indica | 2759 | 32.60% | 22.60% | 44.51% | 0.29% | NA |
| All Japonica | 1512 | 98.90% | 0.10% | 0.86% | 0.07% | NA |
| Aus | 269 | 95.50% | 0.40% | 4.09% | 0.00% | NA |
| Indica I | 595 | 23.40% | 21.50% | 54.79% | 0.34% | NA |
| Indica II | 465 | 47.50% | 15.30% | 37.20% | 0.00% | NA |
| Indica III | 913 | 26.90% | 28.60% | 44.14% | 0.33% | NA |
| Indica Intermediate | 786 | 37.30% | 20.90% | 41.48% | 0.38% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 0.40% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.83% | 0.41% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 6.70% | 23.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0521976073 | C -> T | LOC_Os05g37530.1 | downstream_gene_variant ; 4890.0bp to feature; MODIFIER | silent_mutation | Average:10.26; most accessible tissue: Callus, score: 24.036 | N | N | N | N |
| vg0521976073 | C -> T | LOC_Os05g37550.1 | downstream_gene_variant ; 4014.0bp to feature; MODIFIER | silent_mutation | Average:10.26; most accessible tissue: Callus, score: 24.036 | N | N | N | N |
| vg0521976073 | C -> T | LOC_Os05g37540.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.26; most accessible tissue: Callus, score: 24.036 | N | N | N | N |
| vg0521976073 | C -> DEL | N | N | silent_mutation | Average:10.26; most accessible tissue: Callus, score: 24.036 | N | N | N | N |