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Detailed information for vg0135985532:

Variant ID: vg0135985532 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35985532
Reference Allele: GAlternative Allele: A
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: 327. )

Flanking Sequence (100 bp) in Reference Genome:


TTGGAAAATTGTCCTGTGGACATAAGACATAGTCAAAGATCGCAGTGGCGTTAGTCGAGCATATCATAAATTATTTGGCAGGGAACTTGAAAGCATAAAA[G/A]
GGAAAATTCAGATATATTGAAATTCAAAGAATTCGATTCGTTCTCCTCATATTGAAATTAGAAGGGCAGAGGAAGAAACGGGGTAAACCTTATGATAGCA

Reverse complement sequence

TGCTATCATAAGGTTTACCCCGTTTCTTCCTCTGCCCTTCTAATTTCAATATGAGGAGAACGAATCGAATTCTTTGAATTTCAATATATCTGAATTTTCC[C/T]
TTTTATGCTTTCAAGTTCCCTGCCAAATAATTTATGATATGCTCGACTAACGCCACTGCGATCTTTGACTATGTCTTATGTCCACAGGACAATTTTCCAA

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 99.30% 0.40% 0.25% 0.00% NA
All Indica  2759 98.80% 0.70% 0.43% 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 95.60% 2.70% 1.68% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.40% 0.13% 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

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0135985532 G -> A LOC_Os01g62160.1 intron_variant ; MODIFIER N Average:40.876; most accessible tissue: Callus, score: 65.033 N N N N