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Detailed information for vg1013082033:

Variant ID: vg1013082033 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 13082033
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


CATTACCTTGGAATAATAGTTAAATTTATCTACCCATCTAATCGAACGTGCATGTGGTTACTTCATTGCGTGCATGAATGCTGTTCCTGGTATATATTGC[G/A]
TTGACACTTAGATACACAGGTACACAGGTCTTAAAAAAAGAGCACATAGGAACCAACTAACCTGGTGCGTCTAGGCCGCCTCAACTAAATGTGTTCCATA

Reverse complement sequence

TATGGAACACATTTAGTTGAGGCGGCCTAGACGCACCAGGTTAGTTGGTTCCTATGTGCTCTTTTTTTAAGACCTGTGTACCTGTGTATCTAAGTGTCAA[C/T]
GCAATATATACCAGGAACAGCATTCATGCACGCAATGAAGTAACCACATGCACGTTCGATTAGATGGGTAGATAAATTTAACTATTATTCCAAGGTAATG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.10% 11.70% 0.17% 0.00% NA
All Indica  2759 80.90% 18.80% 0.25% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 92.20% 7.40% 0.37% 0.00% NA
Indica I  595 80.80% 19.00% 0.17% 0.00% NA
Indica II  465 92.90% 6.50% 0.65% 0.00% NA
Indica III  913 78.00% 21.90% 0.11% 0.00% NA
Indica Intermediate  786 77.20% 22.50% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 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 93.30% 6.70% 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
vg1013082033 G -> A LOC_Os10g25300.1 intron_variant ; MODIFIER silent_mutation Average:68.195; most accessible tissue: Minghui63 flower, score: 81.835 N N N N
vg1013082033 G -> A LOC_Os10g25300.2 intron_variant ; MODIFIER silent_mutation Average:68.195; most accessible tissue: Minghui63 flower, score: 81.835 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1013082033 NA 4.60E-09 mr1533 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
vg1013082033 NA 6.70E-09 mr1980 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
vg1013082033 4.50E-06 1.73E-13 mr1533_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
vg1013082033 NA 3.34E-09 mr1980_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