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Detailed information for vg0217282044:

Variant ID: vg0217282044 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 17282044
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


GGCCGGTGGTGCAGCTACCTCTACATGGCTACCGACGTCGCCATCCAGGCCGTTGGTCCCACTACTTCGCCTTCGTCTTCGTCGCCTTCGTCTTCATCCA[G/A]
CATGATTCATCGCCCGTATCTTCCTCGACTACACTTCGCTCTTCTCCGACAATTCTCCGTCTATGCCGTTCTCACGCCGCGACCGTCATTGGCGTATGAT

Reverse complement sequence

ATCATACGCCAATGACGGTCGCGGCGTGAGAACGGCATAGACGGAGAATTGTCGGAGAAGAGCGAAGTGTAGTCGAGGAAGATACGGGCGATGAATCATG[C/T]
TGGATGAAGACGAAGGCGACGAAGACGAAGGCGAAGTAGTGGGACCAACGGCCTGGATGGCGACGTCGGTAGCCATGTAGAGGTAGCTGCACCACCGGCC

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 76.80% 21.40% 1.84% 0.00% NA
All Indica  2759 95.80% 4.10% 0.04% 0.00% NA
All Japonica  1512 37.10% 57.40% 5.49% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 91.20% 8.80% 0.00% 0.00% NA
Indica III  913 94.40% 5.60% 0.00% 0.00% NA
Indica Intermediate  786 97.30% 2.70% 0.00% 0.00% NA
Temperate Japonica  767 62.60% 28.80% 8.60% 0.00% NA
Tropical Japonica  504 5.80% 93.30% 0.99% 0.00% NA
Japonica Intermediate  241 21.60% 73.40% 4.98% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 73.30% 23.30% 3.33% 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
vg0217282044 G -> A LOC_Os02g29160.1 intron_variant ; MODIFIER silent_mutation Average:65.447; most accessible tissue: Zhenshan97 young leaf, score: 81.841 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0217282044 NA 4.18E-06 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
vg0217282044 NA 8.20E-19 mr1518 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
vg0217282044 NA 1.86E-06 mr1355_2 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
vg0217282044 8.51E-06 1.59E-10 mr1749_2 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
vg0217282044 NA 1.70E-11 mr1761_2 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
vg0217282044 NA 5.01E-10 mr1821_2 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