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Detailed information for vg0511003990:

Variant ID: vg0511003990 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 11003990
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


AATGGGTGCATTGGTAGAAGGTTGATGGCTACCACAGGGTGCACTTTGACAAGGTTGATGGCTAGCAATAGGTGTTGAATCAGAGTGGTAAATAACTATC[C/T]
TCCTATCAGTTTCTTCCTCTGCCAGTTCTTTACCCTTACATCCACTACCACCAACCTCATCAACCCCTTTCCCTTTGGATACATCTATATCAACCTCTAT

Reverse complement sequence

ATAGAGGTTGATATAGATGTATCCAAAGGGAAAGGGGTTGATGAGGTTGGTGGTAGTGGATGTAAGGGTAAAGAACTGGCAGAGGAAGAAACTGATAGGA[G/A]
GATAGTTATTTACCACTCTGATTCAACACCTATTGCTAGCCATCAACCTTGTCAAAGTGCACCCTGTGGTAGCCATCAACCTTCTACCAATGCACCCATT

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 94.80% 4.70% 0.53% 0.00% NA
All Indica  2759 91.10% 8.00% 0.91% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.30% 0.17% 0.00% NA
Indica II  465 77.00% 20.20% 2.80% 0.00% NA
Indica III  913 87.70% 11.40% 0.88% 0.00% NA
Indica Intermediate  786 97.10% 2.50% 0.38% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0511003990 C -> T LOC_Os05g18970.1 missense_variant ; p.Arg290Lys; MODERATE nonsynonymous_codon ; R290K Average:49.39; most accessible tissue: Minghui63 young leaf, score: 70.038 benign 0.424 TOLERATED 0.12

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0511003990 3.59E-08 9.29E-36 mr1039 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
vg0511003990 NA 5.38E-20 mr1039 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
vg0511003990 2.22E-13 NA mr1632 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
vg0511003990 5.75E-11 1.73E-12 mr1632 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
vg0511003990 1.02E-11 3.66E-38 mr1039_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
vg0511003990 3.45E-07 1.55E-20 mr1039_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
vg0511003990 NA 3.05E-08 mr1593_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
vg0511003990 1.16E-09 NA mr1632_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
vg0511003990 4.98E-07 3.99E-15 mr1632_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