Search for Variation information by Variation ID:

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

Detailed information for vg1124305955:

Variant ID: vg1124305955 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24305955
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


CGATTCGATTGATTGATTGTAGATTGATTAGTTACAATTGAACCGACCATGTCCCTTATATAGGGGTTGGTCCTGCCCTCTACAGACCCTCCTCCACGTC[C/T]
AACTCGGGATAGAATCCAAAGGAAACCCGAAACATGCCTTCCCGAGTAAGGAAACTTTGAGACCCGACGAAATACACTCGGACTCGGACCCTGCTGGTCA

Reverse complement sequence

TGACCAGCAGGGTCCGAGTCCGAGTGTATTTCGTCGGGTCTCAAAGTTTCCTTACTCGGGAAGGCATGTTTCGGGTTTCCTTTGGATTCTATCCCGAGTT[G/A]
GACGTGGAGGAGGGTCTGTAGAGGGCAGGACCAACCCCTATATAAGGGACATGGTCGGTTCAATTGTAACTAATCAATCTACAATCAATCAATCGAATCG

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 73.30% 26.70% 0.06% 0.00% NA
All Indica  2759 62.30% 37.60% 0.07% 0.00% NA
All Japonica  1512 87.60% 12.40% 0.00% 0.00% NA
Aus  269 92.20% 7.80% 0.00% 0.00% NA
Indica I  595 75.30% 24.70% 0.00% 0.00% NA
Indica II  465 63.40% 36.30% 0.22% 0.00% NA
Indica III  913 53.00% 46.90% 0.11% 0.00% NA
Indica Intermediate  786 62.70% 37.30% 0.00% 0.00% NA
Temperate Japonica  767 94.40% 5.60% 0.00% 0.00% NA
Tropical Japonica  504 78.60% 21.40% 0.00% 0.00% NA
Japonica Intermediate  241 84.60% 15.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 84.40% 14.40% 1.11% 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
vg1124305955 C -> T LOC_Os11g40690.1 intron_variant ; MODIFIER silent_mutation Average:42.856; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124305955 1.97E-06 NA mr1133 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
vg1124305955 NA 5.37E-06 mr1084_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
vg1124305955 NA 3.90E-07 mr1205_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
vg1124305955 3.85E-06 3.85E-06 mr1209_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
vg1124305955 NA 1.00E-06 mr1376_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
vg1124305955 NA 7.90E-07 mr1431_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
vg1124305955 NA 2.41E-06 mr1968_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