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Detailed information for vg0520397801:

Variant ID: vg0520397801 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 20397801
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGGGGGCCCTTGACTTGGAAGGTGCCGGACGAGGAGCTTGCGAAGGAGTCGGTGTAGGAGCCTGAGGAGGAGTCGATGCAGGAGCCTGAGGAGGAGACG[G/A]
TGCAGGAGCATGAGGAGGAGATGGTGCACGAGACGCCGCTTGTCGCCCAGGGAGGATGATGTACCGCTTGCGCCATAGTATAATGGTGTGGCTTGTGTCT

Reverse complement sequence

AGACACAAGCCACACCATTATACTATGGCGCAAGCGGTACATCATCCTCCCTGGGCGACAAGCGGCGTCTCGTGCACCATCTCCTCCTCATGCTCCTGCA[C/T]
CGTCTCCTCCTCAGGCTCCTGCATCGACTCCTCCTCAGGCTCCTACACCGACTCCTTCGCAAGCTCCTCGTCCGGCACCTTCCAAGTCAAGGGCCCCCCA

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 89.00% 11.00% 0.04% 0.04% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 66.90% 32.90% 0.07% 0.13% 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 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 11.90% 87.50% 0.20% 0.40% NA
Japonica Intermediate  241 80.90% 19.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 15.60% 1.11% 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
vg0520397801 G -> DEL LOC_Os05g34420.1 N frameshift_variant Average:44.044; most accessible tissue: Minghui63 young leaf, score: 61.887 N N N N
vg0520397801 G -> A LOC_Os05g34420.1 missense_variant ; p.Pro446Ser; MODERATE nonsynonymous_codon ; P446S Average:44.044; most accessible tissue: Minghui63 young leaf, score: 61.887 unknown unknown TOLERATED 0.11

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0520397801 4.65E-06 1.36E-08 mr1742 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251