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Detailed information for vg0108239676:

Variant ID: vg0108239676 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 8239676
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATAGGCATCAGTATCTTCAACACAAGCTGCCTACGTTTGCCATGGCTGCCGACTGGTTTCTTCACTTCCATGGCTGCATGATTCTGCCAGTGTTGACTG[G/A]
CCTTACCATCTTCATCGCCGGTCGTCTCGTCTGCTGCTGACTAGTGCCCTCACCTCTACGTCTGGTTTATACAGCTACCACTACTGATGGACATCATCGT

Reverse complement sequence

ACGATGATGTCCATCAGTAGTGGTAGCTGTATAAACCAGACGTAGAGGTGAGGGCACTAGTCAGCAGCAGACGAGACGACCGGCGATGAAGATGGTAAGG[C/T]
CAGTCAACACTGGCAGAATCATGCAGCCATGGAAGTGAAGAAACCAGTCGGCAGCCATGGCAAACGTAGGCAGCTTGTGTTGAAGATACTGATGCCTATT

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 99.50% 0.10% 0.44% 0.00% NA
All Indica  2759 99.80% 0.10% 0.14% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 93.70% 0.40% 5.95% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.10% 0.51% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 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
vg0108239676 G -> A LOC_Os01g14730.1 missense_variant ; p.Gly254Asp; MODERATE nonsynonymous_codon ; G254D Average:43.561; most accessible tissue: Zhenshan97 flag leaf, score: 67.31 possibly damaging 1.911 TOLERATED 0.09