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Detailed information for vg0724902343:

Variant ID: vg0724902343 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 24902343
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTTAGGAATAGCACCTTGTCCGGCTTTGCCTTACTCGTGTTCCAATACCCAAGGATATGCTCCCAGATTGGGCCTCCCAAGTATGCACCCTCACGGATG[G/A]
ACTCCCACACATCAGATAATGACATGGTGATGGACTCCCACTGATCATCAGATAATGATGAGGTCTTAGCCTTAGAACAGTTCATGAAATGCCATAAAGA

Reverse complement sequence

TCTTTATGGCATTTCATGAACTGTTCTAAGGCTAAGACCTCATCATTATCTGATGATCAGTGGGAGTCCATCACCATGTCATTATCTGATGTGTGGGAGT[C/T]
CATCCGTGAGGGTGCATACTTGGGAGGCCCAATCTGGGAGCATATCCTTGGGTATTGGAACACGAGTAAGGCAAAGCCGGACAAGGTGCTATTCCTAAAG

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 88.30% 11.50% 0.13% 0.15% NA
All Indica  2759 80.10% 19.50% 0.22% 0.22% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 93.90% 6.10% 0.00% 0.00% NA
Indica II  465 98.10% 1.70% 0.00% 0.22% NA
Indica III  913 55.90% 43.20% 0.44% 0.55% NA
Indica Intermediate  786 87.20% 12.60% 0.25% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 4.40% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0724902343 G -> DEL LOC_Os07g41540.1 N frameshift_variant Average:59.784; most accessible tissue: Callus, score: 75.715 N N N N
vg0724902343 G -> A LOC_Os07g41540.1 missense_variant ; p.Ser55Phe; MODERATE nonsynonymous_codon ; S55F Average:59.784; most accessible tissue: Callus, score: 75.715 probably damaging 2.738 TOLERATED 0.71

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0724902343 3.13E-06 1.72E-06 mr1971 Ind_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
vg0724902343 1.02E-06 2.51E-07 mr1708_2 Ind_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