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Detailed information for vg0314254349:

Variant ID: vg0314254349 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14254349
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTTTTGTCTATCTCCATTTGCTGCTTTGTTCTTTGCTCTGAATTCATTGATATCAATTCTTTTTCTAGCTTGTCAATCTGATCAACTGCAAATTGGAAC[G/A]
AATCAATACTTTTTGATCCTTGTGAGGCTATTTCAGCACATTTCCTTGACAGAATATTGAATCTGAGGACTGAGCTCTCCGATAAAGGTATAATTCTATC

Reverse complement sequence

GATAGAATTATACCTTTATCGGAGAGCTCAGTCCTCAGATTCAATATTCTGTCAAGGAAATGTGCTGAAATAGCCTCACAAGGATCAAAAAGTATTGATT[C/T]
GTTCCAATTTGCAGTTGATCAGATTGACAAGCTAGAAAAAGAATTGATATCAATGAATTCAGAGCAAAGAACAAAGCAGCAAATGGAGATAGACAAAACA

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 97.10% 2.90% 0.00% 0.00% NA
All Indica  2759 98.90% 1.10% 0.00% 0.00% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 71.00% 29.00% 0.00% 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 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.00% 2.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0314254349 G -> A LOC_Os03g24970.1 missense_variant ; p.Ser179Leu; MODERATE nonsynonymous_codon ; S179L Average:4.991; most accessible tissue: Minghui63 flower, score: 7.958 unknown unknown DELETERIOUS 0.02