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Detailed information for vg0141599281:

Variant ID: vg0141599281 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41599281
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


GGTGTTATAAATGTTGCTAATTTTTTCTATAAATTTGGACAAATCTAAATAATTTTGATTGAGAAAAAAAATCAAACGATTTATAATAGAATAAATTTTA[C/T]
AAAACTACATATACTTTGACTAAATTATCATAAAATTACAGATTTAAGGTGATGTATCGTATAACTACATATTTAACAATAAAATTATCACAATACTACA

Reverse complement sequence

TGTAGTATTGTGATAATTTTATTGTTAAATATGTAGTTATACGATACATCACCTTAAATCTGTAATTTTATGATAATTTAGTCAAAGTATATGTAGTTTT[G/A]
TAAAATTTATTCTATTATAAATCGTTTGATTTTTTTTCTCAATCAAAATTATTTAGATTTGTCCAAATTTATAGAAAAAATTAGCAACATTTATAACACC

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 66.20% 33.30% 0.49% 0.00% NA
All Indica  2759 44.00% 55.20% 0.72% 0.00% NA
All Japonica  1512 98.60% 1.40% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 64.90% 33.60% 1.51% 0.00% NA
Indica II  465 24.10% 75.30% 0.65% 0.00% NA
Indica III  913 36.00% 63.70% 0.22% 0.00% NA
Indica Intermediate  786 49.40% 49.90% 0.76% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 96.80% 3.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 3.10% 1.04% 0.00% NA
Intermediate  90 74.40% 23.30% 2.22% 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
vg0141599281 C -> T LOC_Os01g71810.1 upstream_gene_variant ; 4296.0bp to feature; MODIFIER silent_mutation Average:29.48; most accessible tissue: Zhenshan97 root, score: 74.877 N N N N
vg0141599281 C -> T LOC_Os01g71820.1 upstream_gene_variant ; 589.0bp to feature; MODIFIER silent_mutation Average:29.48; most accessible tissue: Zhenshan97 root, score: 74.877 N N N N
vg0141599281 C -> T LOC_Os01g71830.1 upstream_gene_variant ; 4016.0bp to feature; MODIFIER silent_mutation Average:29.48; most accessible tissue: Zhenshan97 root, score: 74.877 N N N N
vg0141599281 C -> T LOC_Os01g71820-LOC_Os01g71830 intergenic_region ; MODIFIER silent_mutation Average:29.48; most accessible tissue: Zhenshan97 root, score: 74.877 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0141599281 NA 5.40E-07 mr1053 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
vg0141599281 9.37E-06 4.37E-11 mr1090 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
vg0141599281 NA 8.08E-06 mr1147 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
vg0141599281 NA 1.51E-06 mr1211 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
vg0141599281 NA 7.08E-06 mr1749 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
vg0141599281 NA 8.29E-07 mr1761 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
vg0141599281 NA 2.39E-08 mr1974 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
vg0141599281 4.61E-06 6.24E-11 mr1974 Ind_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
vg0141599281 2.11E-06 2.11E-06 mr1985 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
vg0141599281 NA 2.59E-07 mr1090_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
vg0141599281 NA 2.31E-09 mr1322_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
vg0141599281 NA 2.96E-08 mr1527_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
vg0141599281 NA 1.62E-07 mr1974_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
vg0141599281 NA 6.35E-07 mr1974_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