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Detailed information for vg1000740409:

Variant ID: vg1000740409 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 740409
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.84, T: 0.16, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


TCAGACCACTTCATCTTGGGTGCAGCCCCCTGCCATGTCGAACAAACCTCACGTTCCACTTTTTTGTATTCTCGCTTTGAAGAGTACACTATGGAGCCTC[T/C]
GAAGATGTGCGAGACATGAAGATCGGAATCTGGGTATGTGAAGTCCGAATCCTGAGTGGTTGCCTCAGTGGCCTTCTCGACTACACGTACTTGCTTGCCC

Reverse complement sequence

GGGCAAGCAAGTACGTGTAGTCGAGAAGGCCACTGAGGCAACCACTCAGGATTCGGACTTCACATACCCAGATTCCGATCTTCATGTCTCGCACATCTTC[A/G]
GAGGCTCCATAGTGTACTCTTCAAAGCGAGAATACAAAAAAGTGGAACGTGAGGTTTGTTCGACATGGCAGGGGGCTGCACCCAAGATGAAGTGGTCTGA

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 42.10% 16.60% 0.87% 40.48% NA
All Indica  2759 53.00% 0.80% 1.16% 44.98% NA
All Japonica  1512 8.90% 48.60% 0.46% 42.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 63.00% 1.00% 1.51% 34.45% NA
Indica II  465 25.40% 0.90% 1.51% 72.26% NA
Indica III  913 55.00% 0.20% 0.44% 44.36% NA
Indica Intermediate  786 59.50% 1.40% 1.53% 37.53% NA
Temperate Japonica  767 10.40% 78.00% 0.65% 10.95% NA
Tropical Japonica  504 3.80% 5.80% 0.40% 90.08% NA
Japonica Intermediate  241 14.90% 44.80% 0.00% 40.25% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 36.70% 20.00% 2.22% 41.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1000740409 T -> C LOC_Os10g02170.1 missense_variant ; p.Arg305Gly; MODERATE nonsynonymous_codon ; R305E Average:22.455; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 benign -0.427 TOLERATED 0.22
vg1000740409 T -> C LOC_Os10g02170.1 missense_variant ; p.Arg305Gly; MODERATE nonsynonymous_codon ; R305G Average:22.455; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 benign -0.339 TOLERATED 1.00
vg1000740409 T -> DEL LOC_Os10g02170.1 N frameshift_variant Average:22.455; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000740409 6.38E-06 NA mr1310 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
vg1000740409 NA 1.68E-08 mr1498 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
vg1000740409 1.78E-06 NA mr1926 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
vg1000740409 3.91E-07 NA mr1926 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
vg1000740409 4.20E-10 NA mr1310_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
vg1000740409 3.80E-09 NA mr1310_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
vg1000740409 2.78E-08 NA mr1959_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