Search for Variation information by Variation ID:

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

Detailed information for vg0505001004:

Variant ID: vg0505001004 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 5001004
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGATTATGGCTGCCTGTTTCTTTGGAAGGAATGTGACGAGGGTTTATTTGTAAAACAGTTTTTACTGTACGTGTAGATCCTAAAATTATATGCACCACAT[G/T]
ATCTCTTCTTGTGCTTATTCTTTATCTTTTTTCTTTTCTTTTCTTTCTTTCAATAACTTCATGCATATTCGAAAGTCTTGAATTTTACCATCCATCTAGC

Reverse complement sequence

GCTAGATGGATGGTAAAATTCAAGACTTTCGAATATGCATGAAGTTATTGAAAGAAAGAAAAGAAAAGAAAAAAGATAAAGAATAAGCACAAGAAGAGAT[C/A]
ATGTGGTGCATATAATTTTAGGATCTACACGTACAGTAAAAACTGTTTTACAAATAAACCCTCGTCACATTCCTTCCAAAGAAACAGGCAGCCATAATCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.50% 13.20% 0.28% 0.00% NA
All Indica  2759 96.90% 3.10% 0.00% 0.00% NA
All Japonica  1512 87.80% 11.40% 0.79% 0.00% NA
Aus  269 2.60% 97.00% 0.37% 0.00% NA
Indica I  595 98.00% 2.00% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 97.40% 2.60% 0.00% 0.00% NA
Indica Intermediate  786 94.70% 5.30% 0.00% 0.00% NA
Temperate Japonica  767 86.70% 11.90% 1.43% 0.00% NA
Tropical Japonica  504 89.30% 10.50% 0.20% 0.00% NA
Japonica Intermediate  241 88.00% 12.00% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0505001004 G -> T LOC_Os05g09020.1 upstream_gene_variant ; 1378.0bp to feature; MODIFIER silent_mutation Average:31.96; most accessible tissue: Callus, score: 61.075 N N N N
vg0505001004 G -> T LOC_Os05g09020.2 upstream_gene_variant ; 1375.0bp to feature; MODIFIER silent_mutation Average:31.96; most accessible tissue: Callus, score: 61.075 N N N N
vg0505001004 G -> T LOC_Os05g09020-LOC_Os05g09030 intergenic_region ; MODIFIER silent_mutation Average:31.96; most accessible tissue: Callus, score: 61.075 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0505001004 NA 4.71E-07 mr1057 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
vg0505001004 NA 7.74E-08 mr1403 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
vg0505001004 NA 1.23E-08 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
vg0505001004 NA 8.69E-08 mr1126_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
vg0505001004 NA 7.60E-09 mr1166_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
vg0505001004 NA 1.64E-06 mr1456_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
vg0505001004 NA 8.79E-08 mr1465_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
vg0505001004 NA 1.51E-06 mr1577_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
vg0505001004 NA 4.33E-14 mr1583_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
vg0505001004 6.81E-07 6.81E-07 mr1587_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
vg0505001004 NA 2.30E-06 mr1792_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
vg0505001004 NA 2.23E-06 mr1929_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