| Variant ID: vg0222980482 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 22980482 |
| Reference Allele: T | Alternative Allele: G,A |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, A: 0.01, others allele: 0.00, population size: 327. )
CCTCGACGTCTCGGGCAACAAGCTGAGGTCTCTCCCCGACAGCATCTCAAAATGCAGGTAGAATCAACCAGCCAAGGCCAAAGCACGCATCATCATCATC[T/G,A]
TCTTCTTCTCCCCAATGGCATCCAGATCCAGTTAAAGAAACTTCAATTCTCGCTAATGGTGATCATCACAAAATGATCCAAACGTACAGGTCGCTGGTGG
CCACCAGCGACCTGTACGTTTGGATCATTTTGTGATGATCACCATTAGCGAGAATTGAAGTTTCTTTAACTGGATCTGGATGCCATTGGGGAGAAGAAGA[A/C,T]
GATGATGATGATGCGTGCTTTGGCCTTGGCTGGTTGATTCTACCTGCATTTTGAGATGCTGTCGGGGAGAGACCTCAGCTTGTTGCCCGAGACGTCGAGG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.80% | 0.10% | 0.06% | 0.00% | A: 0.04% |
| All Indica | 2759 | 99.70% | 0.20% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 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 | 99.00% | 0.80% | 0.25% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 1.11% | 0.00% | A: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0222980482 | T -> A | LOC_Os02g38029.1 | upstream_gene_variant ; 3846.0bp to feature; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> A | LOC_Os02g38050.1 | downstream_gene_variant ; 1364.0bp to feature; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> A | LOC_Os02g38050.4 | downstream_gene_variant ; 1351.0bp to feature; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> A | LOC_Os02g38050.3 | downstream_gene_variant ; 1351.0bp to feature; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> A | LOC_Os02g38050.5 | downstream_gene_variant ; 1351.0bp to feature; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> A | LOC_Os02g38050.6 | downstream_gene_variant ; 1351.0bp to feature; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> A | LOC_Os02g38050.2 | downstream_gene_variant ; 1364.0bp to feature; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> A | LOC_Os02g38040.1 | intron_variant ; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> G | LOC_Os02g38029.1 | upstream_gene_variant ; 3846.0bp to feature; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> G | LOC_Os02g38050.1 | downstream_gene_variant ; 1364.0bp to feature; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> G | LOC_Os02g38050.4 | downstream_gene_variant ; 1351.0bp to feature; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> G | LOC_Os02g38050.3 | downstream_gene_variant ; 1351.0bp to feature; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> G | LOC_Os02g38050.5 | downstream_gene_variant ; 1351.0bp to feature; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> G | LOC_Os02g38050.6 | downstream_gene_variant ; 1351.0bp to feature; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> G | LOC_Os02g38050.2 | downstream_gene_variant ; 1364.0bp to feature; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
| vg0222980482 | T -> G | LOC_Os02g38040.1 | intron_variant ; MODIFIER | N | Average:81.927; most accessible tissue: Callus, score: 87.013 | N | N | N | N |