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Detailed information for vg0728914146:

Variant ID: vg0728914146 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 28914146
Reference Allele: TAlternative Allele: C
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: 109. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTCCGTCCTAAAATATAAGAGATTTTAGATGGATGAGACATATCTTAATACTACGAATATGAATAGATTTTGTCCAGATTTTTAGTATTAGGATATTT[T/C]
ACATATATTTAAAATCTCTTATATTTTGGGACAGTGAGAGTATTATCATGGGGGAGAAATGCAGCTACAATCATTGAACTTAAGCTTGAGATTGATTTTC

Reverse complement sequence

GAAAATCAATCTCAAGCTTAAGTTCAATGATTGTAGCTGCATTTCTCCCCCATGATAATACTCTCACTGTCCCAAAATATAAGAGATTTTAAATATATGT[A/G]
AAATATCCTAATACTAAAAATCTGGACAAAATCTATTCATATTCGTAGTATTAAGATATGTCTCATCCATCTAAAATCTCTTATATTTTAGGACGGACGG

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 64.90% 34.80% 0.04% 0.28% NA
All Indica  2759 96.40% 3.20% 0.04% 0.33% NA
All Japonica  1512 7.30% 92.60% 0.00% 0.13% NA
Aus  269 85.50% 14.50% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 93.10% 5.80% 0.22% 0.86% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 93.00% 6.40% 0.00% 0.64% NA
Temperate Japonica  767 1.60% 98.40% 0.00% 0.00% NA
Tropical Japonica  504 8.90% 90.90% 0.00% 0.20% NA
Japonica Intermediate  241 22.00% 77.60% 0.00% 0.41% NA
VI/Aromatic  96 28.10% 71.90% 0.00% 0.00% NA
Intermediate  90 42.20% 54.40% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0728914146 T -> DEL N N silent_mutation Average:72.587; most accessible tissue: Minghui63 flower, score: 84.277 N N N N
vg0728914146 T -> C LOC_Os07g48380.1 upstream_gene_variant ; 3497.0bp to feature; MODIFIER silent_mutation Average:72.587; most accessible tissue: Minghui63 flower, score: 84.277 N N N N
vg0728914146 T -> C LOC_Os07g48370.1 downstream_gene_variant ; 49.0bp to feature; MODIFIER silent_mutation Average:72.587; most accessible tissue: Minghui63 flower, score: 84.277 N N N N
vg0728914146 T -> C LOC_Os07g48370-LOC_Os07g48380 intergenic_region ; MODIFIER silent_mutation Average:72.587; most accessible tissue: Minghui63 flower, score: 84.277 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0728914146 NA 6.24E-22 mr1021 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
vg0728914146 NA 2.54E-15 mr1165 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
vg0728914146 NA 1.80E-16 mr1323 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
vg0728914146 NA 1.36E-15 mr1324 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
vg0728914146 NA 1.90E-12 mr1325 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
vg0728914146 NA 5.94E-13 mr1326 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
vg0728914146 NA 4.77E-13 mr1335 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
vg0728914146 NA 2.06E-09 mr1336 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
vg0728914146 4.50E-06 8.48E-07 mr1336 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
vg0728914146 NA 1.41E-23 mr1477 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
vg0728914146 NA 1.12E-13 mr1478 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
vg0728914146 NA 9.89E-07 mr1532 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
vg0728914146 NA 1.33E-11 mr1553 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
vg0728914146 NA 1.54E-13 mr1744 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
vg0728914146 NA 6.40E-11 mr1904 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
vg0728914146 NA 4.81E-22 mr1971 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
vg0728914146 4.18E-06 NA mr1971 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
vg0728914146 NA 3.80E-08 mr1299_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
vg0728914146 NA 1.66E-08 mr1700_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
vg0728914146 NA 1.94E-12 mr1713_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
vg0728914146 NA 1.12E-06 mr1727_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
vg0728914146 NA 1.28E-10 mr1756_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
vg0728914146 NA 5.04E-08 mr1837_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
vg0728914146 NA 8.93E-06 mr1840_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
vg0728914146 NA 2.75E-06 mr1915_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