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Detailed information for vg1126454396:

Variant ID: vg1126454396 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26454396
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGCAAATATAAAAAACGAAAAGCTGTGCGTAAAGTACTTTGGATAATAAAGTAAGTCACAGAAAAGTAAATAATAATTCTAAAATTTTTTTGAATAAAA[C/T]
AAGTGGTCAAACACTACAAATAAAAACTTAAAATCCTTTTTATATTATAGTACGGAGGGAGAAATAATTAGGTGATGAGAAAATATAATGGGTGGTGATT

Reverse complement sequence

AATCACCACCCATTATATTTTCTCATCACCTAATTATTTCTCCCTCCGTACTATAATATAAAAAGGATTTTAAGTTTTTATTTGTAGTGTTTGACCACTT[G/A]
TTTTATTCAAAAAAATTTTAGAATTATTATTTACTTTTCTGTGACTTACTTTATTATCCAAAGTACTTTACGCACAGCTTTTCGTTTTTTATATTTGCAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.90% 1.10% 0.00% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 97.70% 2.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 96.60% 3.40% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg1126454396 C -> T LOC_Os11g43800.1 upstream_gene_variant ; 1299.0bp to feature; MODIFIER silent_mutation Average:36.623; most accessible tissue: Minghui63 panicle, score: 86.012 N N N N
vg1126454396 C -> T LOC_Os11g43790.1 downstream_gene_variant ; 515.0bp to feature; MODIFIER silent_mutation Average:36.623; most accessible tissue: Minghui63 panicle, score: 86.012 N N N N
vg1126454396 C -> T LOC_Os11g43790-LOC_Os11g43800 intergenic_region ; MODIFIER silent_mutation Average:36.623; most accessible tissue: Minghui63 panicle, score: 86.012 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126454396 1.02E-07 1.02E-07 mr1191 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
vg1126454396 1.32E-06 1.32E-06 mr1644 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
vg1126454396 2.51E-07 2.51E-07 mr1191_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