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Detailed information for vg0232543553:

Variant ID: vg0232543553 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 32543553
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTGAAATTCCAAAATGGCAAAAGGCAGCATTATTTACACAATACACAGGCCTTAGGGTACGCTCATTTCAGCTTATAGGATTAGATTCTCCTCGTTTTC[C/T]
GTTAGCACGTTTTTCAAACTGCTAAACGGTATATTTCGTACGAAAACTTTCTATAAAGAAGTTATTTAAAAAAATCCAAGAAATTTATTCATCAAAAATT

Reverse complement sequence

AATTTTTGATGAATAAATTTCTTGGATTTTTTTAAATAACTTCTTTATAGAAAGTTTTCGTACGAAATATACCGTTTAGCAGTTTGAAAAACGTGCTAAC[G/A]
GAAAACGAGGAGAATCTAATCCTATAAGCTGAAATGAGCGTACCCTAAGGCCTGTGTATTGTGTAAATAATGCTGCCTTTTGCCATTTTGGAATTTCAAA

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 97.80% 2.00% 0.19% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 93.40% 6.00% 0.60% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 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 89.40% 9.50% 1.04% 0.00% NA
Tropical Japonica  504 98.00% 2.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 3.30% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0232543553 C -> T LOC_Os02g53160.1 upstream_gene_variant ; 1456.0bp to feature; MODIFIER silent_mutation Average:58.394; most accessible tissue: Minghui63 root, score: 81.681 N N N N
vg0232543553 C -> T LOC_Os02g53169.1 upstream_gene_variant ; 2368.0bp to feature; MODIFIER silent_mutation Average:58.394; most accessible tissue: Minghui63 root, score: 81.681 N N N N
vg0232543553 C -> T LOC_Os02g53160-LOC_Os02g53169 intergenic_region ; MODIFIER silent_mutation Average:58.394; most accessible tissue: Minghui63 root, score: 81.681 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0232543553 9.32E-06 9.32E-06 mr1914 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
vg0232543553 4.77E-07 4.77E-07 mr1158_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
vg0232543553 2.80E-06 2.80E-06 mr1186_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
vg0232543553 NA 3.26E-06 mr1321_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
vg0232543553 3.27E-07 3.27E-07 mr1371_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
vg0232543553 NA 5.64E-06 mr1380_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
vg0232543553 4.33E-06 4.33E-06 mr1445_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
vg0232543553 2.55E-07 2.55E-07 mr1499_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
vg0232543553 4.88E-06 4.88E-06 mr1616_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
vg0232543553 9.31E-07 9.31E-07 mr1647_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
vg0232543553 NA 6.50E-06 mr1706_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
vg0232543553 NA 2.18E-06 mr1712_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
vg0232543553 4.18E-07 3.42E-08 mr1946_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
vg0232543553 4.18E-07 3.42E-08 mr1948_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
vg0232543553 NA 3.09E-07 mr1977_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