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Detailed information for vg0135986294:

Variant ID: vg0135986294 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35986294
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.21, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


TGATCTCTGAAAGACTCACTTGAACACCATACAGAGAGGCCTAATGAATCTATACTCCTGGATGATCTATCACATTGAATTATAAAACAGTATTTGCTGT[G/A]
GTACCAGGTACTATAAGATTCAAGAAACTTATCGTGGGAATCCATTTCTCGGAACACATCATTCAACCGACCTACCTTTGAGCCACACTAATCATTTTCT

Reverse complement sequence

AGAAAATGATTAGTGTGGCTCAAAGGTAGGTCGGTTGAATGATGTGTTCCGAGAAATGGATTCCCACGATAAGTTTCTTGAATCTTATAGTACCTGGTAC[C/T]
ACAGCAAATACTGTTTTATAATTCAATGTGATAGATCATCCAGGAGTATAGATTCATTAGGCCTCTCTGTATGGTGTTCAAGTGAGTCTTTCAGAGATCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.50% 33.30% 0.00% 0.28% NA
All Indica  2759 98.50% 1.20% 0.00% 0.36% 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 99.70% 0.00% 0.00% 0.34% NA
Indica II  465 99.40% 0.40% 0.00% 0.22% NA
Indica III  913 99.30% 0.40% 0.00% 0.22% NA
Indica Intermediate  786 96.10% 3.30% 0.00% 0.64% NA
Temperate Japonica  767 1.20% 98.80% 0.00% 0.00% NA
Tropical Japonica  504 3.00% 97.00% 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 47.80% 48.90% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0135986294 G -> A LOC_Os01g62160.1 intron_variant ; MODIFIER silent_mutation Average:43.497; most accessible tissue: Callus, score: 76.692 N N N N
vg0135986294 G -> DEL N N silent_mutation Average:43.497; most accessible tissue: Callus, score: 76.692 N N N N