Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0224541228:

Variant ID: vg0224541228 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24541228
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: 295. )

Flanking Sequence (100 bp) in Reference Genome:


AGAGCTTTCCATCAAGTACTCATGGACCCAAAATGGAGCTCGCATGCATATTTGGCGGCCGTTTGAAGTCGACACTGTAGCAGGTGGCCGAACTGGATTG[C/T]
AGAACTTGGACAGCTTGATCTTGATGTGAACGACGGTTGTATCTATAGTAGCCATGGTCACATCATCCTCCCCTTCTTCACGGAAAACCGTCCTCGGTTT

Reverse complement sequence

AAACCGAGGACGGTTTTCCGTGAAGAAGGGGAGGATGATGTGACCATGGCTACTATAGATACAACCGTCGTTCACATCAAGATCAAGCTGTCCAAGTTCT[G/A]
CAATCCAGTTCGGCCACCTGCTACAGTGTCGACTTCAAACGGCCGCCAAATATGCATGCGAGCTCCATTTTGGGTCCATGAGTACTTGATGGAAAGCTCT

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 87.40% 6.60% 3.51% 2.50% NA
All Indica  2759 87.50% 8.40% 3.91% 0.22% NA
All Japonica  1512 92.60% 0.10% 0.33% 7.01% NA
Aus  269 55.80% 27.50% 15.99% 0.74% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 64.50% 22.60% 12.47% 0.43% NA
Indica III  913 94.40% 4.80% 0.66% 0.11% NA
Indica Intermediate  786 83.70% 10.30% 5.60% 0.38% NA
Temperate Japonica  767 97.50% 0.00% 0.00% 2.48% NA
Tropical Japonica  504 89.50% 0.20% 0.40% 9.92% NA
Japonica Intermediate  241 83.40% 0.00% 1.24% 15.35% NA
VI/Aromatic  96 87.50% 3.10% 8.33% 1.04% NA
Intermediate  90 92.20% 2.20% 2.22% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0224541228 C -> T LOC_Os02g40470.1 missense_variant ; p.Cys294Tyr; MODERATE nonsynonymous_codon ; C294Y Average:47.798; most accessible tissue: Minghui63 panicle, score: 70.194 benign 1.12 DELETERIOUS 0.01
vg0224541228 C -> DEL LOC_Os02g40470.1 N frameshift_variant Average:47.798; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224541228 NA 1.84E-06 mr1069 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
vg0224541228 NA 1.32E-06 mr1130 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
vg0224541228 NA 6.08E-06 mr1149 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
vg0224541228 NA 3.85E-06 mr1202 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
vg0224541228 NA 2.01E-10 mr1072_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
vg0224541228 NA 4.78E-09 mr1075_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
vg0224541228 NA 8.90E-10 mr1077_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
vg0224541228 NA 1.24E-09 mr1149_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
vg0224541228 NA 7.83E-06 mr1406_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
vg0224541228 NA 1.43E-08 mr1441_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
vg0224541228 NA 4.13E-09 mr1861_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
vg0224541228 NA 6.06E-07 mr1878_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