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Detailed information for vg1123185842:

Variant ID: vg1123185842 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23185842
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTGTAGGGCTTCTTTCTATGTTATTGTTTGGTTCTTATGAACAACTATACTATCTACAGTGGTTTCTTTCTCTGTCAAGTGTTATGAACAAATTTATTAC[T/A]
TCATTGCAGATGGTAAGACATTCAAGAAGCCACGTCGCCCTTACGAGAAGGAGCGTCTTGATGCAGAGCTGAAGCTAGTGGGTGAGTATGGACTGAGGTG

Reverse complement sequence

CACCTCAGTCCATACTCACCCACTAGCTTCAGCTCTGCATCAAGACGCTCCTTCTCGTAAGGGCGACGTGGCTTCTTGAATGTCTTACCATCTGCAATGA[A/T]
GTAATAAATTTGTTCATAACACTTGACAGAGAAAGAAACCACTGTAGATAGTATAGTTGTTCATAAGAACCAAACAATAACATAGAAAGAAGCCCTACAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.70% 0.20% 0.02% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 99.30% 0.40% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 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% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 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
vg1123185842 T -> A LOC_Os11g38970.1 upstream_gene_variant ; 3690.0bp to feature; MODIFIER N Average:17.484; most accessible tissue: Zhenshan97 flower, score: 32.793 N N N N
vg1123185842 T -> A LOC_Os11g38959.1 intron_variant ; MODIFIER N Average:17.484; most accessible tissue: Zhenshan97 flower, score: 32.793 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1123185842 NA 2.34E-06 mr1063 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
vg1123185842 NA 6.11E-11 mr1137 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
vg1123185842 NA 4.56E-06 mr1192 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
vg1123185842 5.29E-06 5.21E-12 mr1617 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
vg1123185842 NA 9.49E-07 mr1627 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
vg1123185842 NA 3.70E-06 mr1617_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
vg1123185842 NA 4.83E-06 mr1627_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