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Detailed information for vg1002445363:

Variant ID: vg1002445363 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2445363
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATATCTAGTGACCTACTCCCTCCGTCCCAAAAAAAGGCAAACCCTGGGTTTCCGTGTCCAACTTTGACTGTCCATCTTATATGAATTTTTTTTATAATT[C/T]
GTATTTTCATTGTTGTTAGATAATAAAGCATGATTAATATTTTATGCGTGACTTGTCTTTTTAATTTTTTTCATAATTTTTTCAAATAAGACAGACGGTC

Reverse complement sequence

GACCGTCTGTCTTATTTGAAAAAATTATGAAAAAAATTAAAAAGACAAGTCACGCATAAAATATTAATCATGCTTTATTATCTAACAACAATGAAAATAC[G/A]
AATTATAAAAAAAATTCATATAAGATGGACAGTCAAAGTTGGACACGGAAACCCAGGGTTTGCCTTTTTTTGGGACGGAGGGAGTAGGTCACTAGATATG

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 95.90% 4.00% 0.04% 0.00% NA
All Indica  2759 93.20% 6.70% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 74.80% 25.20% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 95.40% 4.30% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 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 96.70% 3.30% 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
vg1002445363 C -> T LOC_Os10g05010.1 upstream_gene_variant ; 294.0bp to feature; MODIFIER silent_mutation Average:50.256; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg1002445363 C -> T LOC_Os10g05000-LOC_Os10g05010 intergenic_region ; MODIFIER silent_mutation Average:50.256; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002445363 1.52E-08 3.24E-10 mr1709 Ind_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
vg1002445363 NA 8.87E-09 mr1709_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