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Detailed information for vg1126454250:

Variant ID: vg1126454250 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26454250
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTACTAGTATATATATTAGCTTTTTGCTACTCGACTACTCTCTCCATCCCATAATATAAGGGATTTTGAGTTTTGTCTCATAATATAAGGGATTTTGAGT[C/T]
TTTACTTATAGTGTTTGACCACTCGTCTTATTCAAAAAAAAATTTATGCAAATATAAAAAACGAAAAGCTGTGCGTAAAGTACTTTGGATAATAAAGTAA

Reverse complement sequence

TTACTTTATTATCCAAAGTACTTTACGCACAGCTTTTCGTTTTTTATATTTGCATAAATTTTTTTTTGAATAAGACGAGTGGTCAAACACTATAAGTAAA[G/A]
ACTCAAAATCCCTTATATTATGAGACAAAACTCAAAATCCCTTATATTATGGGATGGAGAGAGTAGTCGAGTAGCAAAAAGCTAATATATATACTAGTAC

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 65.00% 33.00% 2.01% 0.00% NA
All Indica  2759 82.20% 15.20% 2.54% 0.00% NA
All Japonica  1512 42.10% 56.50% 1.32% 0.00% NA
Aus  269 40.90% 58.70% 0.37% 0.00% NA
Indica I  595 82.70% 13.40% 3.87% 0.00% NA
Indica II  465 89.90% 7.50% 2.58% 0.00% NA
Indica III  913 84.20% 14.00% 1.75% 0.00% NA
Indica Intermediate  786 75.10% 22.50% 2.42% 0.00% NA
Temperate Japonica  767 63.50% 34.60% 1.96% 0.00% NA
Tropical Japonica  504 15.10% 84.30% 0.60% 0.00% NA
Japonica Intermediate  241 30.70% 68.50% 0.83% 0.00% NA
VI/Aromatic  96 11.50% 88.50% 0.00% 0.00% NA
Intermediate  90 48.90% 46.70% 4.44% 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
vg1126454250 C -> T LOC_Os11g43800.1 upstream_gene_variant ; 1445.0bp to feature; MODIFIER silent_mutation Average:43.17; most accessible tissue: Minghui63 panicle, score: 92.928 N N N N
vg1126454250 C -> T LOC_Os11g43790.1 downstream_gene_variant ; 369.0bp to feature; MODIFIER silent_mutation Average:43.17; most accessible tissue: Minghui63 panicle, score: 92.928 N N N N
vg1126454250 C -> T LOC_Os11g43790-LOC_Os11g43800 intergenic_region ; MODIFIER silent_mutation Average:43.17; most accessible tissue: Minghui63 panicle, score: 92.928 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126454250 NA 8.52E-14 Spikelet_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1126454250 NA 6.07E-07 mr1163 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
vg1126454250 NA 3.51E-06 mr1164 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
vg1126454250 NA 2.76E-07 mr1205 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
vg1126454250 NA 1.77E-06 mr1229 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
vg1126454250 NA 8.07E-09 mr1252 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
vg1126454250 NA 1.84E-07 mr1252 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
vg1126454250 2.24E-07 NA mr1617 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
vg1126454250 NA 1.52E-09 mr1617 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
vg1126454250 NA 7.78E-08 mr1668 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
vg1126454250 NA 1.99E-06 mr1748 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
vg1126454250 NA 3.41E-07 mr1763 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
vg1126454250 NA 1.02E-06 mr1880 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
vg1126454250 NA 2.26E-06 mr1182_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
vg1126454250 NA 2.49E-08 mr1709_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
vg1126454250 NA 9.27E-08 mr1748_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