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Detailed information for vg0135983852:

Variant ID: vg0135983852 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35983852
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 350. )

Flanking Sequence (100 bp) in Reference Genome:


CAAACCAACATGAGAAAATTCCCAAGTGAATTAATTCTTTTTTGTACATGCAGAAGTTAAGCAGTGCCCTAGCAACGGCAAGAGAACACTTTGCGAGATC[T/A]
ATTTTCAGCTGATGGCGTGTCATCCTTCAGGTTGACGATGAGCAAGCCTCAGATAGTGTCTCTGTTAGCAGATCAGTACTCCCAGTTTGCAATGTCCTTT

Reverse complement sequence

AAAGGACATTGCAAACTGGGAGTACTGATCTGCTAACAGAGACACTATCTGAGGCTTGCTCATCGTCAACCTGAAGGATGACACGCCATCAGCTGAAAAT[A/T]
GATCTCGCAAAGTGTTCTCTTGCCGTTGCTAGGGCACTGCTTAACTTCTGCATGTACAAAAAAGAATTAATTCACTTGGGAATTTTCTCATGTTGGTTTG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.70% 0.20% 0.06% 0.00% NA
All Indica  2759 99.50% 0.40% 0.11% 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 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 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
vg0135983852 T -> A LOC_Os01g62160.1 3_prime_UTR_variant ; 535.0bp to feature; MODIFIER N Average:70.226; most accessible tissue: Zhenshan97 flower, score: 84.217 N N N N