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Detailed information for vg0729072157:

Variant ID: vg0729072157 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 29072157
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGGTTTCATTTATGTCTGATTGGTAAAACTTCAGCTCCAGCTTCATCTTTTCTGAAGCTAGAGTCCATCAAACGGTTTCAATTTCACCTAAAAAGAAAG[C/T]
GGAGGGACTAAAGTGCTATCACATAATGAACTAGCGACATGAAGCGGGTTTCAGACTGTTCCACAACTCCATTTCAGAACAAAAAATGCACCTTTTCACA

Reverse complement sequence

TGTGAAAAGGTGCATTTTTTGTTCTGAAATGGAGTTGTGGAACAGTCTGAAACCCGCTTCATGTCGCTAGTTCATTATGTGATAGCACTTTAGTCCCTCC[G/A]
CTTTCTTTTTAGGTGAAATTGAAACCGTTTGATGGACTCTAGCTTCAGAAAAGATGAAGCTGGAGCTGAAGTTTTACCAATCAGACATAAATGAAACCGC

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 98.60% 1.20% 0.19% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.80% 3.60% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 92.20% 6.90% 0.91% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 0.80% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0729072157 C -> T LOC_Os07g48560.1 upstream_gene_variant ; 886.0bp to feature; MODIFIER silent_mutation Average:58.429; most accessible tissue: Minghui63 panicle, score: 85.069 N N N N
vg0729072157 C -> T LOC_Os07g48550-LOC_Os07g48560 intergenic_region ; MODIFIER silent_mutation Average:58.429; most accessible tissue: Minghui63 panicle, score: 85.069 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0729072157 NA 9.51E-06 mr1354 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
vg0729072157 NA 1.53E-06 mr1354_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
vg0729072157 NA 1.76E-06 mr1549_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
vg0729072157 2.66E-06 3.80E-08 mr1679_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
vg0729072157 NA 6.38E-06 mr1723_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
vg0729072157 NA 2.79E-06 mr1757_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