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Detailed information for vg0628765614:

Variant ID: vg0628765614 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 28765614
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: 340. )

Flanking Sequence (100 bp) in Reference Genome:


GTTGACTAACACTCCAGATTGATTGATCAAAGCATTGTGTACGGCGTAGTCACTCGATCTTGGAAATTGTTGAAGAAATCTTGTGCTGTCTCACCATTCC[G/A]
ATTAAGATTTCCTCCTTGTGGCTCATGAGCACCATCACCTTGAACTGCATGTACCCCCTGAGAGCCGTCACCTTGATTCTCTTGAGCCGAGCCATCTAAA

Reverse complement sequence

TTTAGATGGCTCGGCTCAAGAGAATCAAGGTGACGGCTCTCAGGGGGTACATGCAGTTCAAGGTGATGGTGCTCATGAGCCACAAGGAGGAAATCTTAAT[C/T]
GGAATGGTGAGACAGCACAAGATTTCTTCAACAATTTCCAAGATCGAGTGACTACGCCGTACACAATGCTTTGATCAATCAATCTGGAGTGTTAGTCAAC

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 94.60% 5.40% 0.02% 0.00% NA
All Indica  2759 96.80% 3.20% 0.00% 0.00% NA
All Japonica  1512 98.80% 1.10% 0.07% 0.00% NA
Aus  269 75.80% 24.20% 0.00% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 96.60% 3.40% 0.00% 0.00% NA
Indica Intermediate  786 95.20% 4.80% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 97.60% 2.20% 0.20% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 17.70% 82.30% 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
vg0628765614 G -> A LOC_Os06g47510.1 missense_variant ; p.Arg133Trp; MODERATE stop_gained Average:48.011; most accessible tissue: Minghui63 young leaf, score: 75.479 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0628765614 NA 4.60E-06 mr1057 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
vg0628765614 2.44E-06 NA mr1515 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