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Detailed information for vg1121892713:

Variant ID: vg1121892713 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21892713
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACAGAGGGAGTCCATTACACACAAATGGTTCCTACAGATAACTCCTAAGCTGAATCAACACGATCCAGGGTAACTGACCAATGTATTTTCCCTTTGAAG[G/A]
TCTACTCTACCAACCAATATATTTCCCAGCAATACCAGGCCTTGATAATGAAATCGATACGAGCAAATACCAGGCCTTGATAATGAAATCGATACGAAGT

Reverse complement sequence

ACTTCGTATCGATTTCATTATCAAGGCCTGGTATTTGCTCGTATCGATTTCATTATCAAGGCCTGGTATTGCTGGGAAATATATTGGTTGGTAGAGTAGA[C/T]
CTTCAAAGGGAAAATACATTGGTCAGTTACCCTGGATCGTGTTGATTCAGCTTAGGAGTTATCTGTAGGAACCATTTGTGTGTAATGGACTCCCTCTGTT

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 98.60% 1.00% 0.42% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 95.70% 3.00% 1.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 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 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 92.20% 5.50% 2.35% 0.00% NA
Tropical Japonica  504 99.60% 0.20% 0.20% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 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
vg1121892713 G -> A LOC_Os11g37090.1 3_prime_UTR_variant ; 539.0bp to feature; MODIFIER silent_mutation Average:41.533; most accessible tissue: Callus, score: 93.041 N N N N
vg1121892713 G -> A LOC_Os11g37070.1 upstream_gene_variant ; 3970.0bp to feature; MODIFIER silent_mutation Average:41.533; most accessible tissue: Callus, score: 93.041 N N N N
vg1121892713 G -> A LOC_Os11g37070.2 upstream_gene_variant ; 3964.0bp to feature; MODIFIER silent_mutation Average:41.533; most accessible tissue: Callus, score: 93.041 N N N N
vg1121892713 G -> A LOC_Os11g37080.1 downstream_gene_variant ; 305.0bp to feature; MODIFIER silent_mutation Average:41.533; most accessible tissue: Callus, score: 93.041 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121892713 NA 7.72E-10 mr1210 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
vg1121892713 NA 8.20E-10 mr1305 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
vg1121892713 NA 2.71E-06 mr1379 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
vg1121892713 1.72E-08 1.72E-08 mr1409 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
vg1121892713 NA 3.30E-06 mr1515 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
vg1121892713 NA 4.91E-11 mr1585 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
vg1121892713 NA 8.46E-10 mr1586 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
vg1121892713 NA 3.35E-08 mr1765 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
vg1121892713 9.42E-09 6.13E-13 mr1305_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
vg1121892713 7.88E-07 7.24E-09 mr1409_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
vg1121892713 NA 2.24E-06 mr1559_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
vg1121892713 4.06E-07 9.73E-15 mr1585_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
vg1121892713 4.85E-07 8.71E-10 mr1765_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