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Detailed information for vg1125121217:

Variant ID: vg1125121217 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25121217
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.70, C: 0.30, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGAATGCTTACATCCCTGTCCCACCCAGTCTAAGGCATGAACTCGAATGACCCTTAACGCGGCACCATCATCATATTTCCTATGGCAGCATGCCCCAA[C/A]
ACTGCCAAATTCATATGGGAATTAAACTAGCAGGGAGTAGGCAACTCGATTTTTTGATGGCATTGGTACAGCGCAGTGCCAGTGTTGGTAACTATCGCGG

Reverse complement sequence

CCGCGATAGTTACCAACACTGGCACTGCGCTGTACCAATGCCATCAAAAAATCGAGTTGCCTACTCCCTGCTAGTTTAATTCCCATATGAATTTGGCAGT[G/T]
TTGGGGCATGCTGCCATAGGAAATATGATGATGGTGCCGCGTTAAGGGTCATTCGAGTTCATGCCTTAGACTGGGTGGGACAGGGATGTAAGCATTCTAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.10% 32.80% 0.11% 0.00% NA
All Indica  2759 92.60% 7.30% 0.14% 0.00% NA
All Japonica  1512 27.50% 72.40% 0.07% 0.00% NA
Aus  269 46.10% 53.90% 0.00% 0.00% NA
Indica I  595 97.30% 2.40% 0.34% 0.00% NA
Indica II  465 85.40% 14.40% 0.22% 0.00% NA
Indica III  913 97.60% 2.40% 0.00% 0.00% NA
Indica Intermediate  786 87.40% 12.50% 0.13% 0.00% NA
Temperate Japonica  767 8.60% 91.30% 0.13% 0.00% NA
Tropical Japonica  504 55.80% 44.20% 0.00% 0.00% NA
Japonica Intermediate  241 28.60% 71.40% 0.00% 0.00% NA
VI/Aromatic  96 22.90% 77.10% 0.00% 0.00% NA
Intermediate  90 60.00% 40.00% 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
vg1125121217 C -> A LOC_Os11g41800-LOC_Os11g41820 intergenic_region ; MODIFIER silent_mutation Average:48.593; most accessible tissue: Zhenshan97 young leaf, score: 74.675 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125121217 1.32E-14 4.51E-16 mr1238 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
vg1125121217 2.36E-12 3.75E-14 mr1309 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
vg1125121217 NA 2.98E-11 mr1580 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
vg1125121217 NA 1.24E-07 mr1723 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
vg1125121217 4.98E-09 1.03E-10 mr1841 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
vg1125121217 5.40E-07 5.40E-07 mr1900 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
vg1125121217 6.88E-13 3.98E-13 mr1238_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
vg1125121217 NA 6.11E-06 mr1425_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
vg1125121217 3.47E-13 1.89E-13 mr1484_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
vg1125121217 4.48E-16 2.40E-17 mr1841_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
vg1125121217 1.72E-10 4.30E-11 mr1900_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
vg1125121217 4.61E-10 4.61E-10 mr1945_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