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Detailed information for vg0112723315:

Variant ID: vg0112723315 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 12723315
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCAACGGTGACGATGTAGACATCCAACAACGGCGGCATAATAGGCCAGCCGTGTAGGAGGAGGCACCACTCGGCGGCGACGGAGGCAGGCCGGCGGTGAA[G/A]
TCGTAGACGCCCAACAGCGGCGGCATAATAGGCCAGCCGTGTAGGCGGAGGCACCACTCGGCGGCGACGGAGGCAGGCCGGCGGTGGAGTCGTAGACGCC

Reverse complement sequence

GGCGTCTACGACTCCACCGCCGGCCTGCCTCCGTCGCCGCCGAGTGGTGCCTCCGCCTACACGGCTGGCCTATTATGCCGCCGCTGTTGGGCGTCTACGA[C/T]
TTCACCGCCGGCCTGCCTCCGTCGCCGCCGAGTGGTGCCTCCTCCTACACGGCTGGCCTATTATGCCGCCGTTGTTGGATGTCTACATCGTCACCGTTGG

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% 0.10% 0.55% 0.00% NA
All Indica  2759 99.20% 0.00% 0.83% 0.00% NA
All Japonica  1512 99.50% 0.30% 0.20% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.30% 0.00% 0.66% 0.00% NA
Indica Intermediate  786 98.00% 0.00% 2.04% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 0.60% 0.60% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 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
vg0112723315 G -> A LOC_Os01g22620.1 missense_variant ; p.Leu372Phe; MODERATE nonsynonymous_codon ; L372F Average:16.479; most accessible tissue: Zhenshan97 root, score: 27.411 benign 1.265 TOLERATED 0.17