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Detailed information for vg0903742445:

Variant ID: vg0903742445 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 3742445
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TTGGCAGGAGTTCGAACCGGCTCGACTGGTTCACGTGGTGGAACAGGAGCTCGCGGTTCATCTCCAAAACGAATCTCGCCCTCTTCGTGTATGTCCTCGA[C/T]
GACTCTTTCGATCACATTCACTTCGCATGGGGAGTTGGATCCTGAAGATTCCTGGTCATCTAAGTTGTGAAGGACGGAAGGATCGATGTCGATGAATCCG

Reverse complement sequence

CGGATTCATCGACATCGATCCTTCCGTCCTTCACAACTTAGATGACCAGGAATCTTCAGGATCCAACTCCCCATGCGAAGTGAATGTGATCGAAAGAGTC[G/A]
TCGAGGACATACACGAAGAGGGCGAGATTCGTTTTGGAGATGAACCGCGAGCTCCTGTTCCACCACGTGAACCAGTCGAGCCGGTTCGAACTCCTGCCAA

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 92.50% 7.40% 0.06% 0.00% NA
All Indica  2759 95.30% 4.60% 0.11% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 18.60% 81.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 93.10% 6.90% 0.00% 0.00% NA
Indica III  913 96.10% 3.60% 0.33% 0.00% NA
Indica Intermediate  786 92.00% 8.00% 0.00% 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
vg0903742445 C -> T LOC_Os09g07470.1 missense_variant ; p.Val65Ile; MODERATE nonsynonymous_codon ; V65I Average:69.82; most accessible tissue: Zhenshan97 young leaf, score: 84.431 unknown unknown TOLERATED 0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0903742445 NA 4.81E-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
vg0903742445 NA 6.40E-07 mr1803 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
vg0903742445 NA 2.85E-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
vg0903742445 NA 1.80E-17 mr1113_2 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
vg0903742445 NA 6.12E-18 mr1114_2 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
vg0903742445 NA 6.60E-19 mr1117_2 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
vg0903742445 NA 2.05E-17 mr1119_2 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
vg0903742445 NA 3.31E-07 mr1582_2 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