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Detailed information for vg1016323870:

Variant ID: vg1016323870 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 16323870
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATTAATTATAAGGTTGACTCTATTTTTTCTGAACTCTGTTTTTCTCTCACACTATGAATTTAATGTAATTGTTTTACATCAAGTGGATAACTAACTCTT[G/A]
CGTGAGAGCCAACATTTCTTATCTTTCTCTCTCTTTCACATAATAAGTTTATAGTTGGCTTATAGTTTAGCTACCATATGTATGCACGCTCTTATGCACT

Reverse complement sequence

AGTGCATAAGAGCGTGCATACATATGGTAGCTAAACTATAAGCCAACTATAAACTTATTATGTGAAAGAGAGAGAAAGATAAGAAATGTTGGCTCTCACG[C/T]
AAGAGTTAGTTATCCACTTGATGTAAAACAATTACATTAAATTCATAGTGTGAGAGAAAAACAGAGTTCAGAAAAAATAGAGTCAACCTTATAATTAATC

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 97.60% 1.80% 0.66% 0.00% NA
All Indica  2759 95.90% 3.00% 1.12% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 86.60% 9.20% 4.20% 0.00% NA
Indica II  465 98.30% 1.50% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 96.70% 2.70% 0.64% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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  90 100.00% 0.00% 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
vg1016323870 G -> A LOC_Os10g31170.1 intron_variant ; MODIFIER silent_mutation Average:29.345; most accessible tissue: Zhenshan97 panicle, score: 43.098 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1016323870 1.92E-11 1.35E-17 mr1038 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
vg1016323870 9.18E-10 1.99E-17 mr1389 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
vg1016323870 NA 8.85E-07 mr1571 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
vg1016323870 NA 4.75E-06 mr1746 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
vg1016323870 1.33E-13 2.65E-19 mr1038_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
vg1016323870 5.70E-09 NA mr1141_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
vg1016323870 8.48E-10 1.32E-15 mr1389_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
vg1016323870 NA 5.79E-06 mr1887_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