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Detailed information for vg0327810589:

Variant ID: vg0327810589 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 27810589
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:


AAGGCGGTGAGGCCGGGGGAGGAATAGCGAGGTGACTGCGTGCAACGGAGTTCGGACCTGATACGATGCGAACAGAAGAAAACATCCCATGCCAAAATTA[C/T]
CCCTAAACGATATTAGGAGATTATTTACCTGCCCTTTAAAATAAACGGTCAAGATTAATTCTACTTAGAGTAGAATACTGCAAGTAGATTGCACCGGAGC

Reverse complement sequence

GCTCCGGTGCAATCTACTTGCAGTATTCTACTCTAAGTAGAATTAATCTTGACCGTTTATTTTAAAGGGCAGGTAAATAATCTCCTAATATCGTTTAGGG[G/A]
TAATTTTGGCATGGGATGTTTTCTTCTGTTCGCATCGTATCAGGTCCGAACTCCGTTGCACGCAGTCACCTCGCTATTCCTCCCCCGGCCTCACCGCCTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.70% 7.20% 0.83% 0.21% NA
All Indica  2759 95.50% 4.00% 0.51% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 9.70% 77.30% 9.29% 3.72% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 94.40% 5.20% 0.43% 0.00% NA
Indica III  913 92.30% 6.70% 0.99% 0.00% NA
Indica Intermediate  786 96.30% 3.30% 0.38% 0.00% 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 87.50% 12.50% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0327810589 C -> T LOC_Os03g48810.1 upstream_gene_variant ; 1572.0bp to feature; MODIFIER silent_mutation Average:42.949; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0327810589 C -> T LOC_Os03g48780-LOC_Os03g48810 intergenic_region ; MODIFIER silent_mutation Average:42.949; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0327810589 C -> DEL N N silent_mutation Average:42.949; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0327810589 NA 5.40E-06 mr1004 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
vg0327810589 NA 5.82E-07 mr1028 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
vg0327810589 NA 1.61E-07 mr1320 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
vg0327810589 NA 5.13E-06 mr1345 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
vg0327810589 NA 2.04E-08 mr1369 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
vg0327810589 NA 6.34E-07 mr1415 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
vg0327810589 NA 5.61E-07 mr1445 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
vg0327810589 NA 2.90E-08 mr1453 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
vg0327810589 NA 4.46E-06 mr1467 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
vg0327810589 NA 6.34E-07 mr1567 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
vg0327810589 NA 2.40E-07 mr1574 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
vg0327810589 NA 1.45E-07 mr1652 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
vg0327810589 NA 5.10E-06 mr1665 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
vg0327810589 NA 4.18E-07 mr1763 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
vg0327810589 NA 3.30E-07 mr1252_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
vg0327810589 1.68E-07 2.35E-07 mr1263_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
vg0327810589 NA 6.79E-06 mr1740_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