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Detailed information for vg0102107447:

Variant ID: vg0102107447 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2107447
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.03, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


CACAGCTACAAACTTCAATAACCTGATTTGGAAGCCGTGGGCGCCGCATAAGTGCAAAACCTTCGCATGGTTGATCATCCAAAACAGAGTCTGGACATCC[A/G]
ACAGACTGGCCACCAGGGGTTGGCCGAATGGATCCATCTGTCCCTTATGTCGCCATCGCCAAGAGACAGCCATCCACCTCCTCGCGGAGTGTAGATACAC

Reverse complement sequence

GTGTATCTACACTCCGCGAGGAGGTGGATGGCTGTCTCTTGGCGATGGCGACATAAGGGACAGATGGATCCATTCGGCCAACCCCTGGTGGCCAGTCTGT[T/C]
GGATGTCCAGACTCTGTTTTGGATGATCAACCATGCGAAGGTTTTGCACTTATGCGGCGCCCACGGCTTCCAAATCAGGTTATTGAAGTTTGTAGCTGTG

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 64.70% 31.20% 0.06% 4.02% NA
All Indica  2759 71.40% 24.80% 0.11% 3.66% NA
All Japonica  1512 47.00% 48.30% 0.00% 4.63% NA
Aus  269 91.10% 2.20% 0.00% 6.69% NA
Indica I  595 31.60% 67.70% 0.00% 0.67% NA
Indica II  465 93.30% 5.80% 0.22% 0.65% NA
Indica III  913 86.90% 7.40% 0.11% 5.59% NA
Indica Intermediate  786 70.70% 23.70% 0.13% 5.47% NA
Temperate Japonica  767 41.30% 56.60% 0.00% 2.09% NA
Tropical Japonica  504 66.10% 25.20% 0.00% 8.73% NA
Japonica Intermediate  241 25.30% 70.50% 0.00% 4.15% NA
VI/Aromatic  96 72.90% 27.10% 0.00% 0.00% NA
Intermediate  90 66.70% 32.20% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0102107447 A -> G LOC_Os01g04680.1 missense_variant ; p.Asn290Asp; MODERATE nonsynonymous_codon Average:62.589; most accessible tissue: Zhenshan97 young leaf, score: 76.773 possibly damaging -1.641 TOLERATED 1.00
vg0102107447 A -> DEL LOC_Os01g04680.1 N frameshift_variant Average:62.589; most accessible tissue: Zhenshan97 young leaf, score: 76.773 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102107447 NA 2.24E-06 mr1633 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
vg0102107447 NA 9.61E-07 mr1041_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
vg0102107447 NA 6.22E-07 mr1184_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
vg0102107447 NA 3.89E-06 mr1284_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
vg0102107447 NA 9.30E-06 mr1293_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
vg0102107447 NA 4.18E-06 mr1374_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
vg0102107447 NA 7.58E-06 mr1402_2 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
vg0102107447 6.59E-06 6.61E-06 mr1412_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
vg0102107447 NA 6.77E-06 mr1419_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
vg0102107447 NA 7.97E-06 mr1420_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
vg0102107447 NA 3.16E-06 mr1633_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
vg0102107447 NA 1.00E-07 mr1683_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
vg0102107447 NA 1.63E-06 mr1687_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
vg0102107447 NA 6.77E-07 mr1706_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
vg0102107447 NA 1.73E-06 mr1759_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
vg0102107447 2.55E-06 2.55E-06 mr1766_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
vg0102107447 NA 4.11E-07 mr1811_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
vg0102107447 NA 2.08E-06 mr1816_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
vg0102107447 NA 1.64E-06 mr1823_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
vg0102107447 NA 4.54E-07 mr1824_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