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

Detailed information for vg0819150140:

Variant ID: vg0819150140 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19150140
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


GGCGCGGGAGGAAGGATCAAATCAAGTGGGCCGTCGGCTACCGCTCGGCCCAGACGGGAGAGGCGTGACAACCCGCACGTGAAGGGGAAGGATTGGGTCC[A/T]
GTAGCTTCGGGCAAGGTCTATAAATAGATTACCCTTGTACTGAAAGAGGTGAACTGTATTGAACAAACATATTCTAAATACCAATCCTTTCCCCCTCTCC

Reverse complement sequence

GGAGAGGGGGAAAGGATTGGTATTTAGAATATGTTTGTTCAATACAGTTCACCTCTTTCAGTACAAGGGTAATCTATTTATAGACCTTGCCCGAAGCTAC[T/A]
GGACCCAATCCTTCCCCTTCACGTGCGGGTTGTCACGCCTCTCCCGTCTGGGCCGAGCGGTAGCCGACGGCCCACTTGATTTGATCCTTCCTCCCGCGCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.50% 5.80% 1.76% 0.00% NA
All Indica  2759 99.70% 0.20% 0.07% 0.00% NA
All Japonica  1512 77.30% 17.50% 5.22% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 71.30% 20.10% 8.60% 0.00% NA
Tropical Japonica  504 95.40% 4.20% 0.40% 0.00% NA
Japonica Intermediate  241 58.50% 36.90% 4.56% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 3.30% 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
vg0819150140 A -> T LOC_Os08g31010.1 missense_variant ; p.Gln1346Leu; MODERATE nonsynonymous_codon ; Q1346L Average:43.333; most accessible tissue: Minghui63 panicle, score: 56.842 unknown unknown TOLERATED 0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819150140 3.05E-06 NA mr1371_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
vg0819150140 2.45E-06 NA mr1397_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
vg0819150140 8.97E-06 NA mr1445_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
vg0819150140 3.47E-06 3.47E-06 mr1499_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
vg0819150140 3.08E-06 NA mr1645_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
vg0819150140 1.29E-07 NA mr1647_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
vg0819150140 2.51E-06 2.51E-06 mr1647_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
vg0819150140 3.75E-06 3.75E-06 mr1655_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
vg0819150140 NA 9.18E-06 mr1861_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
vg0819150140 2.90E-06 NA mr1970_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
vg0819150140 2.39E-06 NA mr1977_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