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Detailed information for vg0322579188:

Variant ID: vg0322579188 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 22579188
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


ATTGTAAATATCTCTGGATCAATACAACTACTCTTGGCGCATCGCTACCCTCTTTACCGAGGTTTTTACTTATCATCCGGCGGAATTTGGCACCTGACGC[G/A]
GGGCTGCATCGGTTCAGTTTGATCTCCAGCGAAGGGGTAAGTCCTATGTTCCGCTGGCCCTGGTGAATCTATCGGCTACGTTGGTGTTGTTTAAGGTTGC

Reverse complement sequence

GCAACCTTAAACAACACCAACGTAGCCGATAGATTCACCAGGGCCAGCGGAACATAGGACTTACCCCTTCGCTGGAGATCAAACTGAACCGATGCAGCCC[C/T]
GCGTCAGGTGCCAAATTCCGCCGGATGATAAGTAAAAACCTCGGTAAAGAGGGTAGCGATGCGCCAAGAGTAGTTGTATTGATCCAGAGATATTTACAAT

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 94.30% 4.90% 0.17% 0.57% NA
All Indica  2759 98.00% 0.80% 0.29% 0.94% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 23.00% 76.60% 0.00% 0.37% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.60% 0.00% 0.00% 0.43% NA
Indica III  913 97.20% 0.40% 0.44% 1.97% NA
Indica Intermediate  786 96.70% 2.20% 0.38% 0.76% 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 96.90% 3.10% 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
vg0322579188 G -> A LOC_Os03g40610-LOC_Os03g40630 intergenic_region ; MODIFIER silent_mutation Average:39.522; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0322579188 G -> DEL N N silent_mutation Average:39.522; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0322579188 NA 1.64E-16 mr1158 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
vg0322579188 NA 1.25E-12 mr1499 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
vg0322579188 2.80E-06 NA mr1248_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
vg0322579188 NA 7.47E-20 mr1305_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
vg0322579188 2.15E-06 NA mr1406_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
vg0322579188 NA 8.09E-07 mr1603_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
vg0322579188 NA 5.60E-06 mr1608_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
vg0322579188 NA 1.31E-29 mr1757_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
vg0322579188 NA 1.17E-07 mr1762_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
vg0322579188 NA 6.29E-10 mr1818_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
vg0322579188 NA 1.46E-13 mr1846_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
vg0322579188 NA 4.64E-11 mr1897_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
vg0322579188 6.93E-06 2.29E-07 mr1921_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
vg0322579188 NA 3.48E-19 mr1927_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