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Detailed information for vg0607687919:

Variant ID: vg0607687919 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 7687919
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCTAAATGCCGTCCACGCATGCACGCCCAAGTAACCAACGTTAGGGTGGGTTTAGTTAACGCTAAAATTTAAAGTTTGGTTGAAATTGCAACGATGTGA[C/T]
GGAAAAGTTGAAAGTTTATGTGTAGGAAAATTTTGATGTGATATAAAAGTTGGAAGTTTGAAGAAAAAATTTGGAACTAAACTCGGCCTTAGTGTAAATG

Reverse complement sequence

CATTTACACTAAGGCCGAGTTTAGTTCCAAATTTTTTCTTCAAACTTCCAACTTTTATATCACATCAAAATTTTCCTACACATAAACTTTCAACTTTTCC[G/A]
TCACATCGTTGCAATTTCAACCAAACTTTAAATTTTAGCGTTAACTAAACCCACCCTAACGTTGGTTACTTGGGCGTGCATGCGTGGACGGCATTTAGCC

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 99.50% 0.30% 0.17% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 98.60% 0.90% 0.46% 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 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 97.30% 1.80% 0.91% 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 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
vg0607687919 C -> T LOC_Os06g13830-LOC_Os06g13839 intergenic_region ; MODIFIER silent_mutation Average:63.457; most accessible tissue: Minghui63 root, score: 90.092 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0607687919 2.75E-07 2.75E-07 mr1081_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
vg0607687919 NA 6.58E-06 mr1148_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