| Variant ID: vg0503844573 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 3844573 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AAGAGATATATATATCGAGCACAAATTAGGGGAAACACCTTTAAACTCTCAAGAAATATCCCTCCTTTCCTCAGACACCATCCAAACATCCAAACAGTTA[T/C]
GAAAAAAGTCTCAATTTTTTTTACAATATTCATACAACATACATATACCACTTCATAAAATCCTAAGGCTTAATTCAACTCACACATTTTCGAAATAAAA
TTTTATTTCGAAAATGTGTGAGTTGAATTAAGCCTTAGGATTTTATGAAGTGGTATATGTATGTTGTATGAATATTGTAAAAAAAATTGAGACTTTTTTC[A/G]
TAACTGTTTGGATGTTTGGATGGTGTCTGAGGAAAGGAGGGATATTTCTTGAGAGTTTAAAGGTGTTTCCCCTAATTTGTGCTCGATATATATATCTCTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.50% | 8.50% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 97.10% | 2.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 15.20% | 84.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 2.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 18.80% | 81.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0503844573 | T -> C | LOC_Os05g07260.1 | downstream_gene_variant ; 1404.0bp to feature; MODIFIER | silent_mutation | Average:33.991; most accessible tissue: Callus, score: 80.816 | N | N | N | N |
| vg0503844573 | T -> C | LOC_Os05g07260.2 | downstream_gene_variant ; 1415.0bp to feature; MODIFIER | silent_mutation | Average:33.991; most accessible tissue: Callus, score: 80.816 | N | N | N | N |
| vg0503844573 | T -> C | LOC_Os05g07260.4 | downstream_gene_variant ; 1415.0bp to feature; MODIFIER | silent_mutation | Average:33.991; most accessible tissue: Callus, score: 80.816 | N | N | N | N |
| vg0503844573 | T -> C | LOC_Os05g07260.3 | downstream_gene_variant ; 1404.0bp to feature; MODIFIER | silent_mutation | Average:33.991; most accessible tissue: Callus, score: 80.816 | N | N | N | N |
| vg0503844573 | T -> C | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:33.991; most accessible tissue: Callus, score: 80.816 | N | N | N | N |