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Detailed information for vg0624749710:

Variant ID: vg0624749710 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 24749710
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.05, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


CATTAAATCAATAATAATTGAATATATTTTCATAATAAATTTATCTTGGGTTGAAAATATATTTTTTTATAAACTTAGTCAAACTTGACCAAAGTCAAAG[C/T]
GTCTTATAAGCTGAAACGGAGGTAGTACACATTATGCTACGGGACACCAACTACGTAGTTCCCAAACCTTGTGCAGAAATAGTACCCAAAACACAACTCA

Reverse complement sequence

TGAGTTGTGTTTTGGGTACTATTTCTGCACAAGGTTTGGGAACTACGTAGTTGGTGTCCCGTAGCATAATGTGTACTACCTCCGTTTCAGCTTATAAGAC[G/A]
CTTTGACTTTGGTCAAGTTTGACTAAGTTTATAAAAAAATATATTTTCAACCCAAGATAAATTTATTATGAAAATATATTCAATTATTATTGATTTAATG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.30% 41.50% 0.13% 0.00% NA
All Indica  2759 91.20% 8.60% 0.22% 0.00% NA
All Japonica  1512 10.60% 89.40% 0.00% 0.00% NA
Aus  269 11.90% 88.10% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 92.90% 6.90% 0.22% 0.00% NA
Indica III  913 89.00% 10.60% 0.33% 0.00% NA
Indica Intermediate  786 86.00% 13.70% 0.25% 0.00% NA
Temperate Japonica  767 1.30% 98.70% 0.00% 0.00% NA
Tropical Japonica  504 28.00% 72.00% 0.00% 0.00% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 54.40% 45.60% 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
vg0624749710 C -> T LOC_Os06g41340.1 downstream_gene_variant ; 1288.0bp to feature; MODIFIER silent_mutation Average:41.031; most accessible tissue: Callus, score: 83.53 N N N N
vg0624749710 C -> T LOC_Os06g41330-LOC_Os06g41340 intergenic_region ; MODIFIER silent_mutation Average:41.031; most accessible tissue: Callus, score: 83.53 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0624749710 NA 4.17E-25 mr1422 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
vg0624749710 NA 2.51E-06 mr1422 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
vg0624749710 NA 4.95E-22 mr1583 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
vg0624749710 NA 2.12E-08 mr1583 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
vg0624749710 9.86E-06 9.86E-06 mr1848 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
vg0624749710 NA 4.67E-19 mr1218_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
vg0624749710 NA 3.15E-28 mr1422_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
vg0624749710 NA 1.13E-06 mr1422_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
vg0624749710 NA 6.99E-07 mr1548_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
vg0624749710 NA 5.80E-16 mr1583_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
vg0624749710 4.09E-09 1.39E-17 mr1850_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
vg0624749710 4.16E-06 1.28E-09 mr1850_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