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Detailed information for vg0318331646:

Variant ID: vg0318331646 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 18331646
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

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

Flanking Sequence (100 bp) in Reference Genome:


AACAATACTCATATATAGTATGCTCAAAAAGGTTTTTCTTAAAATATACTACCTCCGTTTTTTAATAGATGACGCTGTTGACTTTTTCTCACATGTTTGA[C/T]
CATTCGTTTTATTCAAAAAATTTATGCAAATGTATAAGATATAAATCACACTTAAAGTACTATGAGTGATAAAACAACTCATAACAAAATAAATTATAAT

Reverse complement sequence

ATTATAATTTATTTTGTTATGAGTTGTTTTATCACTCATAGTACTTTAAGTGTGATTTATATCTTATACATTTGCATAAATTTTTTGAATAAAACGAATG[G/A]
TCAAACATGTGAGAAAAAGTCAACAGCGTCATCTATTAAAAAACGGAGGTAGTATATTTTAAGAAAAACCTTTTTGAGCATACTATATATGAGTATTGTT

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 44.50% 15.70% 3.60% 36.23% NA
All Indica  2759 15.70% 19.50% 5.91% 58.86% NA
All Japonica  1512 86.30% 12.90% 0.20% 0.60% NA
Aus  269 82.20% 0.00% 0.37% 17.47% NA
Indica I  595 41.50% 5.70% 3.36% 49.41% NA
Indica II  465 7.50% 23.40% 8.82% 60.22% NA
Indica III  913 3.00% 29.70% 4.71% 62.65% NA
Indica Intermediate  786 15.80% 15.90% 7.51% 60.81% NA
Temperate Japonica  767 99.70% 0.00% 0.13% 0.13% NA
Tropical Japonica  504 62.90% 35.50% 0.40% 1.19% NA
Japonica Intermediate  241 92.50% 6.60% 0.00% 0.83% NA
VI/Aromatic  96 96.90% 0.00% 0.00% 3.12% NA
Intermediate  90 56.70% 7.80% 3.33% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0318331646 C -> T LOC_Os03g32050.1 intron_variant ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0318331646 C -> DEL N N silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0318331646 NA 1.71E-07 mr1217 Jap_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
vg0318331646 2.76E-09 1.08E-10 mr1439 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
vg0318331646 2.09E-07 2.14E-08 mr1439 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
vg0318331646 NA 4.81E-07 mr1845 Jap_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
vg0318331646 NA 2.57E-07 mr1852 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
vg0318331646 NA 4.16E-08 mr1852 Jap_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
vg0318331646 NA 2.04E-06 mr1188_2 Jap_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