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Detailed information for vg0215134070:

Variant ID: vg0215134070 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 15134070
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGAGAATCTCAGAGCGGAGTACTCCGATCCATGGCGGCTTCTCCGCCACTGCCTACTTCCATCGATGGTGGTCAAGTGCTAGATGACATGGAGGTCGTG[G/A]
AGATGAAGTACCTGTTTGGCAAGGTCCTGATGCCAAGCGACGTGTCCTGGGACACCGAACAGCTCGTGATCCCGGACGAGCACGTCGGGAAACTACTGGA

Reverse complement sequence

TCCAGTAGTTTCCCGACGTGCTCGTCCGGGATCACGAGCTGTTCGGTGTCCCAGGACACGTCGCTTGGCATCAGGACCTTGCCAAACAGGTACTTCATCT[C/T]
CACGACCTCCATGTCATCTAGCACTTGACCACCATCGATGGAAGTAGGCAGTGGCGGAGAAGCCGCCATGGATCGGAGTACTCCGCTCTGAGATTCTCTC

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 99.60% 0.40% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 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
vg0215134070 G -> A LOC_Os02g25830.1 missense_variant ; p.Glu24Lys; MODERATE nonsynonymous_codon ; E24K Average:82.618; most accessible tissue: Minghui63 flag leaf, score: 87.594 unknown unknown TOLERATED 0.21