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Detailed information for vg1124756478:

Variant ID: vg1124756478 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24756478
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGACCAGGAGTTCTCGAGCTCGATATCCTTCGCTCTCGTCCGGACCGCCGGCGCCGGCGACAATGTCCGTCTCCATGCGAGAGCCAAGATCAGCTTGCTC[G/A]
ACCTCGCCGGCGAGCCGGTGGCACGGTACAGCCAACCCGTCGACAAGTGTTCCACCTCCAAGGCAAGCGATCCATGGGTTTGCAAGAGCTTCATCGAGAG

Reverse complement sequence

CTCTCGATGAAGCTCTTGCAAACCCATGGATCGCTTGCCTTGGAGGTGGAACACTTGTCGACGGGTTGGCTGTACCGTGCCACCGGCTCGCCGGCGAGGT[C/T]
GAGCAAGCTGATCTTGGCTCTCGCATGGAGACGGACATTGTCGCCGGCGCCGGCGGTCCGGACGAGAGCGAAGGATATCGAGCTCGAGAACTCCTGGTCG

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 96.50% 3.50% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 89.20% 10.80% 0.00% 0.00% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 95.60% 4.40% 0.00% 0.00% NA
Tropical Japonica  504 78.20% 21.80% 0.00% 0.00% NA
Japonica Intermediate  241 92.10% 7.90% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg1124756478 G -> A LOC_Os11g41300.1 missense_variant ; p.Asp105Asn; MODERATE nonsynonymous_codon ; D105N Average:76.193; most accessible tissue: Minghui63 flag leaf, score: 85.151 unknown unknown TOLERATED 0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124756478 5.64E-06 3.70E-07 mr1238 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124756478 NA 6.68E-06 mr1900 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124756478 4.81E-08 7.40E-10 mr1238_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124756478 2.07E-07 2.07E-07 mr1484_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124756478 NA 2.64E-07 mr1841_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124756478 NA 4.96E-07 mr1900_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124756478 4.88E-09 4.88E-09 mr1945_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251