Variant ID: vg0234310894 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 34310894 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 295. )
CCTATGAAGATAATATACCTATACCTATGGAATTCCTCTACTTATTCTACTGTAGTTGGTAATTTTCTTCATTTTTTTTAAGATAATGAAATAACATTCC[G/A]
GCTTTTGCTCAACGAGATACAACCAATTATTACAAAGTCCACACACGAACAAACTCAGCACACACTGACATAATGTAAAGAAAACATAAACTAAAAGACA
TGTCTTTTAGTTTATGTTTTCTTTACATTATGTCAGTGTGTGCTGAGTTTGTTCGTGTGTGGACTTTGTAATAATTGGTTGTATCTCGTTGAGCAAAAGC[C/T]
GGAATGTTATTTCATTATCTTAAAAAAAATGAAGAAAATTACCAACTACAGTAGAATAAGTAGAGGAATTCCATAGGTATAGGTATATTATCTTCATAGG
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 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
All Indica | 2759 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Aus | 269 | 64.70% | 35.30% | 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 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 93.80% | 6.20% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0234310894 | G -> A | LOC_Os02g56040.1 | upstream_gene_variant ; 3165.0bp to feature; MODIFIER | silent_mutation | Average:36.789; most accessible tissue: Callus, score: 59.39 | N | N | N | N |
vg0234310894 | G -> A | LOC_Os02g56060.1 | upstream_gene_variant ; 1812.0bp to feature; MODIFIER | silent_mutation | Average:36.789; most accessible tissue: Callus, score: 59.39 | N | N | N | N |
vg0234310894 | G -> A | LOC_Os02g56050.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.789; most accessible tissue: Callus, score: 59.39 | N | N | N | N |