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Detailed information for vg0622510881:

Variant ID: vg0622510881 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 22510881
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


GATCGCTACGTGAGTAAGGGGTGTCTTCGTTTGATAGGAGGATGCTAGGGTCAACCGTCACCGTGAAAGGGGGTTGCCCATCAAACTGATTGTAATCCTC[G/A]
TCAGTCTTGTCCTCTACTCCGATGATTTTTCTTTTGCCTGGGAGAACCACGTGGCGCTTCGGCTCGTCAGGCCCTTTGCCCTTCTTTCCTTTGCTAGACA

Reverse complement sequence

TGTCTAGCAAAGGAAAGAAGGGCAAAGGGCCTGACGAGCCGAAGCGCCACGTGGTTCTCCCAGGCAAAAGAAAAATCATCGGAGTAGAGGACAAGACTGA[C/T]
GAGGATTACAATCAGTTTGATGGGCAACCCCCTTTCACGGTGACGGTTGACCCTAGCATCCTCCTATCAAACGAAGACACCCCTTACTCACGTAGCGATC

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 61.10% 38.20% 0.78% 0.00% NA
All Indica  2759 39.20% 60.00% 0.76% 0.00% NA
All Japonica  1512 96.30% 2.70% 0.99% 0.00% NA
Aus  269 74.70% 25.30% 0.00% 0.00% NA
Indica I  595 16.60% 83.40% 0.00% 0.00% NA
Indica II  465 29.00% 71.00% 0.00% 0.00% NA
Indica III  913 61.30% 36.80% 1.86% 0.00% NA
Indica Intermediate  786 36.60% 62.80% 0.51% 0.00% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 92.30% 4.80% 2.98% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 63.30% 35.60% 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
vg0622510881 G -> A LOC_Os06g38070.1 synonymous_variant ; p.Asp878Asp; LOW synonymous_codon Average:16.349; most accessible tissue: Minghui63 young leaf, score: 29.964 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0622510881 2.43E-06 1.10E-08 mr1064 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
vg0622510881 NA 7.49E-06 mr1229 Ind_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
vg0622510881 NA 4.49E-06 mr1285 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
vg0622510881 1.62E-06 6.54E-07 mr1289 Ind_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
vg0622510881 NA 1.02E-12 mr1329 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
vg0622510881 4.88E-06 4.87E-06 mr1329 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
vg0622510881 NA 9.62E-06 mr1344 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
vg0622510881 NA 8.75E-08 mr1408 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
vg0622510881 NA 6.25E-06 mr1408 Ind_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
vg0622510881 NA 3.56E-07 mr1534 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
vg0622510881 NA 3.09E-06 mr1981 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