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Detailed information for vg0525520857:

Variant ID: vg0525520857 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 25520857
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATCCCTTCTGACATCCGGTCAAACGTCCGATGTGACACCTAAAAATTTTCATTTCGTGAACTAAACGAGGCCTAAAACGTGGTCGGCTCAAGAGTCGTC[C/T]
ACAGTCATGCAGTGAAGACCCATGCAGAACCACAATACTAGCCTAGCATGGGCTCACCTGACAGTGTGTGTAAATATAATAAATATCCCAATCTATCTAT

Reverse complement sequence

ATAGATAGATTGGGATATTTATTATATTTACACACACTGTCAGGTGAGCCCATGCTAGGCTAGTATTGTGGTTCTGCATGGGTCTTCACTGCATGACTGT[G/A]
GACGACTCTTGAGCCGACCACGTTTTAGGCCTCGTTTAGTTCACGAAATGAAAATTTTTAGGTGTCACATCGGACGTTTGACCGGATGTCAGAAGGGATT

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 91.10% 4.00% 4.85% 0.00% NA
All Indica  2759 85.00% 6.90% 8.19% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 61.70% 14.50% 23.87% 0.00% NA
Indica II  465 95.30% 0.90% 3.87% 0.00% NA
Indica III  913 93.80% 5.30% 0.99% 0.00% NA
Indica Intermediate  786 86.30% 6.50% 7.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 2.20% 3.33% 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
vg0525520857 C -> T LOC_Os05g43880.1 upstream_gene_variant ; 4653.0bp to feature; MODIFIER silent_mutation Average:51.386; most accessible tissue: Minghui63 root, score: 62.438 N N N N
vg0525520857 C -> T LOC_Os05g43880-LOC_Os05g43890 intergenic_region ; MODIFIER silent_mutation Average:51.386; most accessible tissue: Minghui63 root, score: 62.438 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0525520857 NA 8.00E-06 mr1285 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
vg0525520857 NA 7.08E-06 mr1528 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
vg0525520857 NA 3.44E-09 mr1547 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
vg0525520857 NA 5.30E-07 mr1547 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
vg0525520857 NA 3.33E-12 mr1739 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
vg0525520857 NA 1.29E-09 mr1739 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
vg0525520857 NA 2.90E-06 mr1255_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