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Detailed information for vg0918927566:

Variant ID: vg0918927566 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 18927566
Reference Allele: TAlternative Allele: C,TAA
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


AAGATATTGCATGTGGGTTATAAATGCTTGTGAGCATGGATGCATGTATCAATGTCTATTTACTCCAATGCACAAATAACGAATAGACTTAATAAATAAA[T/C,TAA]
ATAAATATGTAGATCAATTTAGAATTAAGAGAGTATAATTAAGTAACGTAGAGAAACAAGGCCCTAGAGAGTTTCTGGCAGCTTTACTCTGAGAATAATT

Reverse complement sequence

AATTATTCTCAGAGTAAAGCTGCCAGAAACTCTCTAGGGCCTTGTTTCTCTACGTTACTTAATTATACTCTCTTAATTCTAAATTGATCTACATATTTAT[A/G,TTA]
TTTATTTATTAAGTCTATTCGTTATTTGTGCATTGGAGTAAATAGACATTGATACATGCATCCATGCTCACAAGCATTTATAACCCACATGCAATATCTT

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 75.00% 23.40% 1.48% 0.00% TAA: 0.11%
All Indica  2759 97.00% 2.90% 0.07% 0.00% NA
All Japonica  1512 38.90% 56.80% 4.30% 0.00% NA
Aus  269 79.20% 18.60% 0.37% 0.00% TAA: 1.86%
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 97.20% 2.80% 0.00% 0.00% NA
Indica Intermediate  786 96.30% 3.40% 0.25% 0.00% NA
Temperate Japonica  767 19.70% 75.50% 4.82% 0.00% NA
Tropical Japonica  504 65.50% 31.20% 3.37% 0.00% NA
Japonica Intermediate  241 44.40% 51.00% 4.56% 0.00% NA
VI/Aromatic  96 15.60% 84.40% 0.00% 0.00% NA
Intermediate  90 60.00% 37.80% 2.22% 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
vg0918927566 T -> C LOC_Os09g31438-LOC_Os09g31442 intergenic_region ; MODIFIER silent_mutation Average:45.074; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N
vg0918927566 T -> TAA LOC_Os09g31438-LOC_Os09g31442 intergenic_region ; MODIFIER silent_mutation Average:45.074; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0918927566 6.42E-06 NA mr1023 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
vg0918927566 1.31E-06 NA mr1079 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
vg0918927566 1.62E-07 NA mr1142 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
vg0918927566 3.97E-06 NA mr1178 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
vg0918927566 8.56E-09 NA mr1489 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
vg0918927566 7.00E-07 NA mr1491 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
vg0918927566 NA 1.99E-06 mr1677 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
vg0918927566 4.68E-08 NA mr1778 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
vg0918927566 2.19E-06 NA mr1023_2 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
vg0918927566 5.20E-06 NA mr1057_2 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
vg0918927566 NA 6.79E-10 mr1057_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
vg0918927566 NA 1.31E-06 mr1182_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
vg0918927566 1.46E-07 NA mr1489_2 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
vg0918927566 2.06E-06 NA mr1778_2 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
vg0918927566 NA 2.72E-08 mr1905_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
vg0918927566 NA 1.74E-06 mr1980_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