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Detailed information for vg1119855883:

Variant ID: vg1119855883 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 19855883
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTATTTTAATTAACCAACCCCATTGCGGTGGCACTATTCCAAAACTATTGCCAATAGTCAAAGTCTATGCTTTAATGTGATCCCCTTTTGTGCACTAGTT[A/G]
AACTAAGCATGGCTAAGCATCTCCTAAACCAACATCTAGTCGTTTTAATACCCAAGTTATCAATGGCGTAAGGGAAACAACATATAGCTGAGTAATAGGA

Reverse complement sequence

TCCTATTACTCAGCTATATGTTGTTTCCCTTACGCCATTGATAACTTGGGTATTAAAACGACTAGATGTTGGTTTAGGAGATGCTTAGCCATGCTTAGTT[T/C]
AACTAGTGCACAAAAGGGGATCACATTAAAGCATAGACTTTGACTATTGGCAATAGTTTTGGAATAGTGCCACCGCAATGGGGTTGGTTAATTAAAATAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 25.80% 1.80% 16.36% 56.12% NA
All Indica  2759 8.10% 1.10% 21.67% 69.19% NA
All Japonica  1512 51.00% 2.80% 5.82% 40.41% NA
Aus  269 39.40% 0.00% 26.39% 34.20% NA
Indica I  595 9.70% 0.00% 14.45% 75.80% NA
Indica II  465 3.40% 0.60% 19.35% 76.56% NA
Indica III  913 6.50% 0.90% 31.00% 61.66% NA
Indica Intermediate  786 11.50% 2.30% 17.68% 68.58% NA
Temperate Japonica  767 78.70% 2.00% 1.43% 17.86% NA
Tropical Japonica  504 17.90% 4.20% 13.49% 64.48% NA
Japonica Intermediate  241 32.00% 2.50% 3.73% 61.83% NA
VI/Aromatic  96 84.40% 7.30% 3.12% 5.21% NA
Intermediate  90 41.10% 5.60% 14.44% 38.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1119855883 A -> DEL N N silent_mutation Average:8.201; most accessible tissue: Minghui63 flag leaf, score: 12.986 N N N N
vg1119855883 A -> G LOC_Os11g33970.1 upstream_gene_variant ; 2722.0bp to feature; MODIFIER silent_mutation Average:8.201; most accessible tissue: Minghui63 flag leaf, score: 12.986 N N N N
vg1119855883 A -> G LOC_Os11g33934-LOC_Os11g33970 intergenic_region ; MODIFIER silent_mutation Average:8.201; most accessible tissue: Minghui63 flag leaf, score: 12.986 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1119855883 NA 2.40E-07 mr1179 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
vg1119855883 NA 2.25E-09 mr1549 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
vg1119855883 NA 7.87E-06 mr1596 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
vg1119855883 NA 2.88E-11 mr1624 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
vg1119855883 NA 6.29E-06 mr1624 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
vg1119855883 NA 5.60E-06 mr1729 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
vg1119855883 NA 4.44E-08 mr1757 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
vg1119855883 NA 8.23E-06 mr1871 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
vg1119855883 NA 6.61E-07 mr1038_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
vg1119855883 NA 5.01E-07 mr1042_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
vg1119855883 NA 8.10E-09 mr1092_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
vg1119855883 NA 3.22E-08 mr1152_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
vg1119855883 NA 1.70E-07 mr1154_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
vg1119855883 NA 4.45E-06 mr1389_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
vg1119855883 NA 5.92E-07 mr1389_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
vg1119855883 NA 3.23E-10 mr1624_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
vg1119855883 NA 9.64E-06 mr1624_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
vg1119855883 NA 1.27E-09 mr1746_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