| Variant ID: vg0234310851 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34310851 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 300. )
AGAAAACCGGCCTCTACATCCACGACAAGTACATTTACATGTACCTATGAAGATAATATACCTATACCTATGGAATTCCTCTACTTATTCTACTGTAGTT[G/A]
GTAATTTTCTTCATTTTTTTTAAGATAATGAAATAACATTCCGGCTTTTGCTCAACGAGATACAACCAATTATTACAAAGTCCACACACGAACAAACTCA
TGAGTTTGTTCGTGTGTGGACTTTGTAATAATTGGTTGTATCTCGTTGAGCAAAAGCCGGAATGTTATTTCATTATCTTAAAAAAAATGAAGAAAATTAC[C/T]
AACTACAGTAGAATAAGTAGAGGAATTCCATAGGTATAGGTATATTATCTTCATAGGTACATGTAAATGTACTTGTCGTGGATGTAGAGGCCGGTTTTCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.00% | 0.90% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 97.10% | 2.80% | 0.07% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 91.30% | 8.50% | 0.20% | 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 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0234310851 | G -> A | LOC_Os02g56040.1 | upstream_gene_variant ; 3122.0bp to feature; MODIFIER | silent_mutation | Average:39.396; most accessible tissue: Callus, score: 59.39 | N | N | N | N |
| vg0234310851 | G -> A | LOC_Os02g56060.1 | upstream_gene_variant ; 1855.0bp to feature; MODIFIER | silent_mutation | Average:39.396; most accessible tissue: Callus, score: 59.39 | N | N | N | N |
| vg0234310851 | G -> A | LOC_Os02g56050.1 | intron_variant ; MODIFIER | silent_mutation | Average:39.396; most accessible tissue: Callus, score: 59.39 | N | N | N | N |