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Detailed information for vg0602358935:

Variant ID: vg0602358935 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 2358935
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, T: 0.10, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


CGGGTAGCAAATGGTTCACTTCATAGCCAAAGCTCCAACTGGAGGATAAATTTTGCCTTCACTAGCTAATGGTCAGTGGTAAATATGATTGGTTGGTGAT[T/G]
ATCAGAAATTTCAGCTGTGTACCCACTTGCCAGGCATTTTCAATAATGTTTTTGAGGAAAAGGCTGTATAATCGTATACATAAGTATTGATGTTGTCCAT

Reverse complement sequence

ATGGACAACATCAATACTTATGTATACGATTATACAGCCTTTTCCTCAAAAACATTATTGAAAATGCCTGGCAAGTGGGTACACAGCTGAAATTTCTGAT[A/C]
ATCACCAACCAATCATATTTACCACTGACCATTAGCTAGTGAAGGCAAAATTTATCCTCCAGTTGGAGCTTTGGCTATGAAGTGAACCATTTGCTACCCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.30% 40.40% 0.00% 0.36% NA
All Indica  2759 87.50% 12.00% 0.00% 0.51% NA
All Japonica  1512 1.30% 98.60% 0.00% 0.13% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 98.70% 0.80% 0.00% 0.50% NA
Indica II  465 53.10% 46.20% 0.00% 0.65% NA
Indica III  913 98.00% 1.80% 0.00% 0.22% NA
Indica Intermediate  786 87.00% 12.20% 0.00% 0.76% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 1.80% 97.80% 0.00% 0.40% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 79.20% 20.80% 0.00% 0.00% NA
Intermediate  90 41.10% 57.80% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0602358935 T -> G LOC_Os06g05240.1 intron_variant ; MODIFIER silent_mutation Average:65.223; most accessible tissue: Callus, score: 90.182 N N N N
vg0602358935 T -> DEL N N silent_mutation Average:65.223; most accessible tissue: Callus, score: 90.182 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0602358935 NA 3.79E-06 mr1044 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
vg0602358935 NA 3.48E-13 mr1069 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
vg0602358935 1.12E-25 3.03E-104 mr1141 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
vg0602358935 3.62E-19 5.91E-43 mr1141 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
vg0602358935 NA 7.37E-14 mr1149 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
vg0602358935 NA 1.06E-21 mr1150 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
vg0602358935 NA 7.22E-07 mr1183 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
vg0602358935 NA 6.20E-08 mr1439 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
vg0602358935 NA 1.07E-14 mr1441 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
vg0602358935 NA 8.18E-06 mr1598 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
vg0602358935 NA 1.53E-14 mr1982 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
vg0602358935 6.57E-24 2.81E-113 mr1141_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
vg0602358935 2.09E-16 2.74E-41 mr1141_2 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
vg0602358935 NA 6.84E-27 mr1149_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
vg0602358935 NA 4.75E-09 mr1222_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
vg0602358935 NA 1.49E-27 mr1441_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
vg0602358935 NA 1.21E-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