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Detailed information for vg0135986131:

Variant ID: vg0135986131 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35986131
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary 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: 286. )

Flanking Sequence (100 bp) in Reference Genome:


GAATAAATATCACTAACGACTTCAAGAATTCAAAAATATATTGTCTATGTTTTTGTAAGAACATGTATGATCAAAATAAGAATACAGCAGCCAGACAAAT[A/G]
GCTATACAAATCTACTTTATTTGTTCAAGCTAAATTGTACTTGTATGGGCTGCTTCACCCAATGATCTCTGAAAGACTCACTTGAACACCATACAGAGAG

Reverse complement sequence

CTCTCTGTATGGTGTTCAAGTGAGTCTTTCAGAGATCATTGGGTGAAGCAGCCCATACAAGTACAATTTAGCTTGAACAAATAAAGTAGATTTGTATAGC[T/C]
ATTTGTCTGGCTGCTGTATTCTTATTTTGATCATACATGTTCTTACAAAAACATAGACAATATATTTTTGAATTCTTGAAGTCGTTAGTGATATTTATTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.70% 33.20% 0.04% 0.00% NA
All Indica  2759 98.70% 1.20% 0.07% 0.00% NA
All Japonica  1512 2.10% 97.90% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 96.40% 3.30% 0.25% 0.00% NA
Temperate Japonica  767 1.30% 98.70% 0.00% 0.00% NA
Tropical Japonica  504 2.80% 97.20% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 96.70% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 0.00% 0.00% NA
Intermediate  90 53.30% 46.70% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0135986131 A -> G LOC_Os01g62160.1 intron_variant ; MODIFIER silent_mutation Average:35.956; most accessible tissue: Callus, score: 51.778 N N N N