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Detailed information for vg0404582911:

Variant ID: vg0404582911 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 4582911
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAAGTTATATAGACAAATGACCAAAATAAAAGTTGTATATCTTGATGAGAGGATCAACTTTTTTGTTGACCATATTTCCATTTGAAATCATTTAGTATC[C/T]
GAAAATGTATTATGACTAATAAAATGAATTATTACACAACAGCTATATATTTTGTACGCACAAATATAAAGACTTGTTTGGAAAAATGGGAAAATAGTCA

Reverse complement sequence

TGACTATTTTCCCATTTTTCCAAACAAGTCTTTATATTTGTGCGTACAAAATATATAGCTGTTGTGTAATAATTCATTTTATTAGTCATAATACATTTTC[G/A]
GATACTAAATGATTTCAAATGGAAATATGGTCAACAAAAAAGTTGATCCTCTCATCAAGATATACAACTTTTATTTTGGTCATTTGTCTATATAACTTTG

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 95.20% 4.70% 0.17% 0.00% NA
All Indica  2759 98.00% 1.70% 0.29% 0.00% NA
All Japonica  1512 92.20% 7.80% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.10% 0.40% 0.43% 0.00% NA
Indica III  913 95.80% 3.60% 0.55% 0.00% NA
Indica Intermediate  786 98.60% 1.40% 0.00% 0.00% NA
Temperate Japonica  767 94.50% 5.50% 0.00% 0.00% NA
Tropical Japonica  504 85.90% 14.10% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 49.00% 51.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0404582911 C -> T LOC_Os04g08480.1 upstream_gene_variant ; 3344.0bp to feature; MODIFIER silent_mutation Average:19.53; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg0404582911 C -> T LOC_Os04g08480-LOC_Os04g08500 intergenic_region ; MODIFIER silent_mutation Average:19.53; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0404582911 2.50E-06 NA mr1549 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
vg0404582911 3.77E-07 NA 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
vg0404582911 1.65E-06 3.06E-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