\

Search for Variation information by Variation ID:

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

Detailed information for vg0110444462:

Variant ID: vg0110444462 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 10444462
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCTAACCTGGTCTTGGTCTGGAACCCCTCTCGTTGGCATATGGTGAACCTGTGTCGGCTTCCGAAATGCCTTGTCATGAAAGCCTCAAGGTCTCCAGAC[A/G]
TGGCCGTTCTGCACGGGCTGGGTGATCCGGGTTAGTAATGTCGTGTGGGTAAAGTGCACCCCCTCTGCAGAGGTTATTAAACTGTTCGAACAGCCGTGCC

Reverse complement sequence

GGCACGGCTGTTCGAACAGTTTAATAACCTCTGCAGAGGGGGTGCACTTTACCCACACGACATTACTAACCCGGATCACCCAGCCCGTGCAGAACGGCCA[T/C]
GTCTGGAGACCTTGAGGCTTTCATGACAAGGCATTTCGGAAGCCGACACAGGTTCACCATATGCCAACGAGAGGGGTTCCAGACCAAGACCAGGTTAGGT

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 61.20% 32.70% 0.47% 5.67% NA
All Indica  2759 93.80% 1.10% 0.54% 4.60% NA
All Japonica  1512 3.30% 96.60% 0.00% 0.07% NA
Aus  269 46.80% 0.70% 2.23% 50.19% NA
Indica I  595 98.00% 1.20% 0.34% 0.50% NA
Indica II  465 98.50% 0.40% 0.22% 0.86% NA
Indica III  913 90.70% 1.10% 0.66% 7.56% NA
Indica Intermediate  786 91.30% 1.40% 0.76% 6.49% NA
Temperate Japonica  767 1.80% 98.20% 0.00% 0.00% NA
Tropical Japonica  504 5.20% 94.60% 0.00% 0.20% NA
Japonica Intermediate  241 4.10% 95.90% 0.00% 0.00% NA
VI/Aromatic  96 85.40% 13.50% 0.00% 1.04% NA
Intermediate  90 52.20% 42.20% 1.11% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0110444462 A -> G LOC_Os01g18530-LOC_Os01g18550 intergenic_region ; MODIFIER silent_mutation Average:37.759; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 N N N N
vg0110444462 A -> DEL N N silent_mutation Average:37.759; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0110444462 NA 3.58E-07 mr1162 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
vg0110444462 NA 9.56E-50 mr1519 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
vg0110444462 NA 2.21E-42 mr1591 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
vg0110444462 NA 4.40E-23 mr1888 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
vg0110444462 NA 5.24E-06 mr1020_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
vg0110444462 NA 7.19E-32 mr1102_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
vg0110444462 NA 1.70E-39 mr1152_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
vg0110444462 NA 8.36E-14 mr1191_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
vg0110444462 NA 3.49E-41 mr1223_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
vg0110444462 NA 6.51E-45 mr1519_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
vg0110444462 NA 4.81E-42 mr1944_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