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Detailed information for vg0902019555:

Variant ID: vg0902019555 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 2019555
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


CTACAAGAGGATGGCCAAATAGCGGAGTGTGCCTCCTATGCCGTATGACGAACGAGACGGCATGCCACCTTTTAGCTTCCTGTAGATACACCAGAAGGAT[C/T]
TGGAGACTGACGGCCAACTGGGTGGCTTATCAGCAATTGGATCCGAGCAATTGGGAGCCATGCCAAAGCGTACACGAATAGTGGGAAATGTTAGCCAATA

Reverse complement sequence

TATTGGCTAACATTTCCCACTATTCGTGTACGCTTTGGCATGGCTCCCAATTGCTCGGATCCAATTGCTGATAAGCCACCCAGTTGGCCGTCAGTCTCCA[G/A]
ATCCTTCTGGTGTATCTACAGGAAGCTAAAAGGTGGCATGCCGTCTCGTTCGTCATACGGCATAGGAGGCACACTCCGCTATTTGGCCATCCTCTTGTAG

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 93.50% 6.30% 0.15% 0.00% NA
All Indica  2759 96.60% 3.20% 0.25% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 23.80% 76.20% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 95.10% 4.90% 0.00% 0.00% NA
Indica III  913 97.60% 2.10% 0.33% 0.00% NA
Indica Intermediate  786 93.60% 5.90% 0.51% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 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
vg0902019555 C -> T LOC_Os09g03939.1 intron_variant ; MODIFIER silent_mutation Average:33.542; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 N N N N
vg0902019555 C -> T LOC_Os09g03939.2 intron_variant ; MODIFIER silent_mutation Average:33.542; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0902019555 NA 5.01E-06 mr1006 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
vg0902019555 NA 1.02E-06 mr1007 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
vg0902019555 NA 6.70E-06 mr1052 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
vg0902019555 NA 3.61E-10 mr1722 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
vg0902019555 NA 8.37E-06 mr1808 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
vg0902019555 6.86E-06 NA mr1010_2 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