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Detailed information for vg1127976664:

Variant ID: vg1127976664 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27976664
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACAGTTCATTGAATTTTCAACTTCACATGTTAAATGTATTATTTCTATCAGGTTATTGATACGTGTATACTATTATTATATGGATGGCATTAGCAACGA[G/T]
GCGGTTCATTAAAATTATCGAAATAGTACATTGAGCATGTGAAGTTTGAATCTTATGAGCACATATATTTTACTTGCAGGGTCTTTGTAAACAATCTTGT

Reverse complement sequence

ACAAGATTGTTTACAAAGACCCTGCAAGTAAAATATATGTGCTCATAAGATTCAAACTTCACATGCTCAATGTACTATTTCGATAATTTTAATGAACCGC[C/A]
TCGTTGCTAATGCCATCCATATAATAATAGTATACACGTATCAATAACCTGATAGAAATAATACATTTAACATGTGAAGTTGAAAATTCAATGAACTGTA

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 46.60% 3.60% 1.10% 48.73% NA
All Indica  2759 46.20% 3.70% 0.87% 49.18% NA
All Japonica  1512 45.80% 3.50% 1.59% 49.14% NA
Aus  269 58.70% 0.40% 0.74% 40.15% NA
Indica I  595 59.70% 0.00% 0.34% 40.00% NA
Indica II  465 19.10% 0.00% 1.08% 79.78% NA
Indica III  913 52.90% 10.50% 1.10% 35.49% NA
Indica Intermediate  786 44.40% 0.80% 0.89% 53.94% NA
Temperate Japonica  767 38.60% 6.10% 1.30% 53.98% NA
Tropical Japonica  504 56.90% 0.00% 1.98% 41.07% NA
Japonica Intermediate  241 45.20% 2.50% 1.66% 50.62% NA
VI/Aromatic  96 21.90% 12.50% 2.08% 63.54% NA
Intermediate  90 58.90% 3.30% 0.00% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127976664 G -> T LOC_Os11g46190.1 upstream_gene_variant ; 1829.0bp to feature; MODIFIER silent_mutation Average:30.267; most accessible tissue: Zhenshan97 root, score: 79.962 N N N N
vg1127976664 G -> T LOC_Os11g46200.1 downstream_gene_variant ; 1704.0bp to feature; MODIFIER silent_mutation Average:30.267; most accessible tissue: Zhenshan97 root, score: 79.962 N N N N
vg1127976664 G -> T LOC_Os11g46190-LOC_Os11g46200 intergenic_region ; MODIFIER silent_mutation Average:30.267; most accessible tissue: Zhenshan97 root, score: 79.962 N N N N
vg1127976664 G -> DEL N N silent_mutation Average:30.267; most accessible tissue: Zhenshan97 root, score: 79.962 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127976664 8.39E-07 1.62E-10 mr1549_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
vg1127976664 NA 2.46E-09 mr1757_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