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Detailed information for vg0135985694:

Variant ID: vg0135985694 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35985694
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


AAGGGCAGAGGAAGAAACGGGGTAAACCTTATGATAGCAAATTTAACAGAAGAGATTCAAATCTAATAGAACATGGTCCACAAGTGTCGAGAACAGAAAA[T/A]
GAACAATACTAGCAATATCATGAATGAACTGAGCATATTATATGAGAAAAGGTTTAGCTGTTTTGGCAATACAGTGAATATCGATTCAAAATTTAGAAGA

Reverse complement sequence

TCTTCTAAATTTTGAATCGATATTCACTGTATTGCCAAAACAGCTAAACCTTTTCTCATATAATATGCTCAGTTCATTCATGATATTGCTAGTATTGTTC[A/T]
TTTTCTGTTCTCGACACTTGTGGACCATGTTCTATTAGATTTGAATCTCTTCTGTTAAATTTGCTATCATAAGGTTTACCCCGTTTCTTCCTCTGCCCTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.70% 33.20% 0.08% 0.00% NA
All Indica  2759 98.70% 1.20% 0.14% 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% 0.00% 0.17% 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 96.30% 3.30% 0.38% 0.00% 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 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 0.00% 0.00% NA
Intermediate  90 54.40% 45.60% 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
vg0135985694 T -> A LOC_Os01g62160.1 intron_variant ; MODIFIER silent_mutation Average:34.247; most accessible tissue: Callus, score: 57.796 N N N N