Variant ID: vg0222980452 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 22980452 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTCCATAGGCCTCCTCACCAGCCTCAAGATCCTCGACGTCTCGGGCAACAAGCTGAGGTCTCTCCCCGACAGCATCTCAAAATGCAGGTAGAATCAACCA[G/A]
CCAAGGCCAAAGCACGCATCATCATCATCTTCTTCTTCTCCCCAATGGCATCCAGATCCAGTTAAAGAAACTTCAATTCTCGCTAATGGTGATCATCACA
TGTGATGATCACCATTAGCGAGAATTGAAGTTTCTTTAACTGGATCTGGATGCCATTGGGGAGAAGAAGAAGATGATGATGATGCGTGCTTTGGCCTTGG[C/T]
TGGTTGATTCTACCTGCATTTTGAGATGCTGTCGGGGAGAGACCTCAGCTTGTTGCCCGAGACGTCGAGGATCTTGAGGCTGGTGAGGAGGCCTATGGAG
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 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
All Indica | 2759 | 99.20% | 0.80% | 0.00% | 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 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 98.60% | 1.40% | 0.00% | 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 | 100.00% | 0.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0222980452 | G -> A | LOC_Os02g38029.1 | upstream_gene_variant ; 3816.0bp to feature; MODIFIER | N | Average:79.798; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
vg0222980452 | G -> A | LOC_Os02g38050.1 | downstream_gene_variant ; 1394.0bp to feature; MODIFIER | N | Average:79.798; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
vg0222980452 | G -> A | LOC_Os02g38050.4 | downstream_gene_variant ; 1381.0bp to feature; MODIFIER | N | Average:79.798; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
vg0222980452 | G -> A | LOC_Os02g38050.3 | downstream_gene_variant ; 1381.0bp to feature; MODIFIER | N | Average:79.798; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
vg0222980452 | G -> A | LOC_Os02g38050.5 | downstream_gene_variant ; 1381.0bp to feature; MODIFIER | N | Average:79.798; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
vg0222980452 | G -> A | LOC_Os02g38050.6 | downstream_gene_variant ; 1381.0bp to feature; MODIFIER | N | Average:79.798; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
vg0222980452 | G -> A | LOC_Os02g38050.2 | downstream_gene_variant ; 1394.0bp to feature; MODIFIER | N | Average:79.798; most accessible tissue: Callus, score: 87.013 | N | N | N | N |
vg0222980452 | G -> A | LOC_Os02g38040.1 | intron_variant ; MODIFIER | N | Average:79.798; most accessible tissue: Callus, score: 87.013 | N | N | N | N |