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Detailed information for vg0135985648:

Variant ID: vg0135985648 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35985648
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


ATTGAAATTCAAAGAATTCGATTCGTTCTCCTCATATTGAAATTAGAAGGGCAGAGGAAGAAACGGGGTAAACCTTATGATAGCAAATTTAACAGAAGAG[A/G]
TTCAAATCTAATAGAACATGGTCCACAAGTGTCGAGAACAGAAAATGAACAATACTAGCAATATCATGAATGAACTGAGCATATTATATGAGAAAAGGTT

Reverse complement sequence

AACCTTTTCTCATATAATATGCTCAGTTCATTCATGATATTGCTAGTATTGTTCATTTTCTGTTCTCGACACTTGTGGACCATGTTCTATTAGATTTGAA[T/C]
CTCTTCTGTTAAATTTGCTATCATAAGGTTTACCCCGTTTCTTCCTCTGCCCTTCTAATTTCAATATGAGGAGAACGAATCGAATTCTTTGAATTTCAAT

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 66.50% 33.30% 0.13% 0.11% NA
All Indica  2759 98.50% 1.20% 0.18% 0.11% 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% 0.34% 0.00% NA
Indica II  465 99.40% 0.40% 0.00% 0.22% NA
Indica III  913 99.50% 0.40% 0.11% 0.00% NA
Indica Intermediate  786 96.10% 3.40% 0.25% 0.25% NA
Temperate Japonica  767 1.20% 98.80% 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 50.00% 46.70% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0135985648 A -> G LOC_Os01g62160.1 intron_variant ; MODIFIER silent_mutation Average:34.441; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 N N N N
vg0135985648 A -> DEL N N silent_mutation Average:34.441; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 N N N N