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Detailed information for vg0624461841:

Variant ID: vg0624461841 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 24461841
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTTTAATCCAAATTGCGTCATGATTTGACAATATGGTGCTACATTAAACATTTACTAATGACAGATTAATTAGGCTTAATAAATTCGTCTCGCAGTTT[C/T]
CTGGTGGAATCTGTAAATTTTTTTTGTTATTGGACTATATTCAATACTTCAAATATGTGCTGGTATATCCGATGTGACAACCAAGTCCAAAAATTTTCCC

Reverse complement sequence

GGGAAAATTTTTGGACTTGGTTGTCACATCGGATATACCAGCACATATTTGAAGTATTGAATATAGTCCAATAACAAAAAAAATTTACAGATTCCACCAG[G/A]
AAACTGCGAGACGAATTTATTAAGCCTAATTAATCTGTCATTAGTAAATGTTTAATGTAGCACCATATTGTCAAATCATGACGCAATTTGGATTAAAAGA

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 85.50% 14.40% 0.04% 0.00% NA
All Indica  2759 98.40% 1.60% 0.00% 0.00% NA
All Japonica  1512 65.00% 34.90% 0.13% 0.00% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 98.50% 1.50% 0.00% 0.00% NA
Indica Intermediate  786 97.30% 2.70% 0.00% 0.00% NA
Temperate Japonica  767 88.40% 11.60% 0.00% 0.00% NA
Tropical Japonica  504 38.90% 61.10% 0.00% 0.00% NA
Japonica Intermediate  241 45.20% 53.90% 0.83% 0.00% NA
VI/Aromatic  96 15.60% 84.40% 0.00% 0.00% NA
Intermediate  90 76.70% 23.30% 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
vg0624461841 C -> T LOC_Os06g40970.1 intron_variant ; MODIFIER silent_mutation Average:44.798; most accessible tissue: Minghui63 flower, score: 69.56 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0624461841 NA 3.74E-06 mr1183 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
vg0624461841 NA 4.39E-06 mr1503 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
vg0624461841 NA 4.29E-07 mr1180_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
vg0624461841 1.42E-07 NA mr1181_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
vg0624461841 9.08E-07 9.08E-07 mr1181_2 Jap_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
vg0624461841 NA 8.68E-07 mr1183_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
vg0624461841 NA 9.96E-09 mr1794_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