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Detailed information for vg1123834004:

Variant ID: vg1123834004 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23834004
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCAAACCAATCACAAAAGGGAAAAACTCACACACCAACAGCAATTTCCAAAGTGTTCACTAAAACTACGCTAAGGAATCACCTCACATCCTCCCATGACC[G/A]
TGGGCACGGCTGTTCGAATAGTTATTAACCTCTGCAGAAGGGGTACACTTTACCCACACGACGTTACTAACCCCGAATCACCCAGCCCGCGACTCTCGGT

Reverse complement sequence

ACCGAGAGTCGCGGGCTGGGTGATTCGGGGTTAGTAACGTCGTGTGGGTAAAGTGTACCCCTTCTGCAGAGGTTAATAACTATTCGAACAGCCGTGCCCA[C/T]
GGTCATGGGAGGATGTGAGGTGATTCCTTAGCGTAGTTTTAGTGAACACTTTGGAAATTGCTGTTGGTGTGTGAGTTTTTCCCTTTTGTGATTGGTTTGA

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 70.00% 1.00% 7.60% 21.39% NA
All Indica  2759 58.60% 1.50% 10.91% 29.03% NA
All Japonica  1512 90.60% 0.00% 2.05% 7.34% NA
Aus  269 62.50% 1.90% 8.18% 27.51% NA
Indica I  595 74.60% 0.00% 1.34% 24.03% NA
Indica II  465 38.50% 3.40% 28.17% 29.89% NA
Indica III  913 58.40% 0.70% 7.23% 33.73% NA
Indica Intermediate  786 58.50% 2.40% 12.21% 26.84% NA
Temperate Japonica  767 96.10% 0.00% 0.65% 3.26% NA
Tropical Japonica  504 86.90% 0.00% 2.98% 10.12% NA
Japonica Intermediate  241 80.90% 0.00% 4.56% 14.52% NA
VI/Aromatic  96 93.80% 0.00% 0.00% 6.25% NA
Intermediate  90 71.10% 2.20% 5.56% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1123834004 G -> A LOC_Os11g39960-LOC_Os11g39990 intergenic_region ; MODIFIER silent_mutation Average:36.38; most accessible tissue: Callus, score: 67.175 N N N N
vg1123834004 G -> DEL N N silent_mutation Average:36.38; most accessible tissue: Callus, score: 67.175 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1123834004 NA 6.18E-07 mr1238 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
vg1123834004 NA 3.49E-06 mr1279 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
vg1123834004 NA 2.83E-07 mr1113_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
vg1123834004 NA 7.29E-08 mr1114_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
vg1123834004 NA 1.67E-07 mr1238_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
vg1123834004 NA 1.96E-06 mr1484_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
vg1123834004 NA 4.79E-06 mr1609_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
vg1123834004 NA 2.41E-06 mr1841_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
vg1123834004 NA 1.19E-06 mr1900_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