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Detailed information for vg0329241236:

Variant ID: vg0329241236 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 29241236
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGCTCAATTTCATAGGAAAATAAGCAAGAGGTTCAACCTCTTGGAAACTATCATTTTACTTTGTTTGTTTCCTATGGTGCTATCAAAGAGACCCTCTT[C/T]
ATATTTCCTGTGTTTTTCATTCCTATAGGATTAGAAAAACATACCACTCCAATTCCTATGTTTTTTCTATTCCTTTGTTTTTCCTATCCTACGTTTCAAA

Reverse complement sequence

TTTGAAACGTAGGATAGGAAAAACAAAGGAATAGAAAAAACATAGGAATTGGAGTGGTATGTTTTTCTAATCCTATAGGAATGAAAAACACAGGAAATAT[G/A]
AAGAGGGTCTCTTTGATAGCACCATAGGAAACAAACAAAGTAAAATGATAGTTTCCAAGAGGTTGAACCTCTTGCTTATTTTCCTATGAAATTGAGCTAT

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 85.50% 14.50% 0.04% 0.00% NA
All Indica  2759 83.00% 16.90% 0.07% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 33.50% 66.50% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 93.30% 6.70% 0.00% 0.00% NA
Indica III  913 59.90% 39.90% 0.22% 0.00% NA
Indica Intermediate  786 91.10% 8.90% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 75.00% 25.00% 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
vg0329241236 C -> T LOC_Os03g51110.1 downstream_gene_variant ; 2854.0bp to feature; MODIFIER silent_mutation Average:53.41; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0329241236 C -> T LOC_Os03g51120.1 downstream_gene_variant ; 1398.0bp to feature; MODIFIER silent_mutation Average:53.41; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0329241236 C -> T LOC_Os03g51110-LOC_Os03g51120 intergenic_region ; MODIFIER silent_mutation Average:53.41; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0329241236 NA 1.61E-06 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
vg0329241236 NA 3.74E-06 mr1057 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
vg0329241236 NA 2.86E-06 mr1073 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
vg0329241236 NA 2.78E-06 mr1153 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
vg0329241236 NA 2.64E-07 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
vg0329241236 NA 5.20E-08 mr1393 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
vg0329241236 NA 2.88E-08 mr1403 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
vg0329241236 NA 7.02E-07 mr1417 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
vg0329241236 NA 2.61E-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
vg0329241236 NA 2.30E-06 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
vg0329241236 NA 1.78E-11 mr1612 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
vg0329241236 NA 1.31E-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
vg0329241236 NA 4.41E-08 mr1706 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
vg0329241236 NA 2.59E-11 mr1730 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
vg0329241236 NA 2.11E-08 mr1989 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