| Variant ID: vg0128724188 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724188 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
GCTGTCCGAATGACCCTCCGATGGGATGGGTCATACCTACCTCCACTTCGCTGGAAGCAGATGCAACGTGGGAGCACGGTTTGTCTGCTGATGACGTGAC[C/T]
GGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGTCGCACGTCTGTCCTTCTTCATACAATGACTTCTTTGCAATGG
CCATTGCAAAGAAGTCATTGTATGAAGAAGGACAGACGTGCGACATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCC[G/A]
GTCACGTCATCAGCAGACAAACCGTGCTCCCACGTTGCATCTGCTTCCAGCGAAGTGGAGGTAGGTATGACCCATCCCATCGGAGGGTCATTCGGACAGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.00% | 0.00% | 3.15% | 26.81% | NA |
| All Indica | 2759 | 60.60% | 0.00% | 1.45% | 37.98% | NA |
| All Japonica | 1512 | 88.90% | 0.00% | 0.93% | 10.19% | NA |
| Aus | 269 | 66.50% | 0.00% | 30.86% | 2.60% | NA |
| Indica I | 595 | 50.60% | 0.00% | 1.34% | 48.07% | NA |
| Indica II | 465 | 52.00% | 0.00% | 1.08% | 46.88% | NA |
| Indica III | 913 | 72.60% | 0.00% | 0.55% | 26.83% | NA |
| Indica Intermediate | 786 | 59.20% | 0.00% | 2.80% | 38.04% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 70.00% | 0.00% | 2.58% | 27.38% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 0.41% | 4.56% | NA |
| VI/Aromatic | 96 | 50.00% | 0.00% | 9.38% | 40.62% | NA |
| Intermediate | 90 | 75.60% | 0.00% | 3.33% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724188 | C -> T | LOC_Os01g49990.1 | synonymous_variant ; p.Thr27Thr; LOW | N | Average:10.888; most accessible tissue: Callus, score: 22.262 | N | N | N | N |
| vg0128724188 | C -> T | LOC_Os01g49980.1 | upstream_gene_variant ; 803.0bp to feature; MODIFIER | N | Average:10.888; most accessible tissue: Callus, score: 22.262 | N | N | N | N |
| vg0128724188 | C -> T | LOC_Os01g50010.1 | upstream_gene_variant ; 4789.0bp to feature; MODIFIER | N | Average:10.888; most accessible tissue: Callus, score: 22.262 | N | N | N | N |
| vg0128724188 | C -> T | LOC_Os01g50000.1 | downstream_gene_variant ; 2401.0bp to feature; MODIFIER | N | Average:10.888; most accessible tissue: Callus, score: 22.262 | N | N | N | N |