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Detailed information for vg1001243731:

Variant ID: vg1001243731 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1243731
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.08, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


AATTTCTATGCTTTCCTCTTCTGCTGTTGTGGGTGCTGTAGGCCGTTCATCCAATATTTCTTTGACCAATGTATGTTGCTGTTCTGATGACAAAAGAGTT[T/C]
GCAACAATTCCATAGGATGCTTCCCCATTACCACCTCTAGAACAACAACACCAAAGCTATAAACATCACATTTCTCTGTCACGACACATGTGAAGGACAG

Reverse complement sequence

CTGTCCTTCACATGTGTCGTGACAGAGAAATGTGATGTTTATAGCTTTGGTGTTGTTGTTCTAGAGGTGGTAATGGGGAAGCATCCTATGGAATTGTTGC[A/G]
AACTCTTTTGTCATCAGAACAGCAACATACATTGGTCAAAGAAATATTGGATGAACGGCCTACAGCACCCACAACAGCAGAAGAGGAAAGCATAGAAATT

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 38.00% 36.80% 0.53% 24.71% NA
All Indica  2759 51.20% 6.60% 0.83% 41.36% NA
All Japonica  1512 5.90% 93.10% 0.07% 0.99% NA
Aus  269 94.80% 4.80% 0.00% 0.37% NA
Indica I  595 42.40% 2.90% 0.50% 54.29% NA
Indica II  465 65.40% 4.70% 0.65% 29.25% NA
Indica III  913 52.50% 8.30% 0.44% 38.77% NA
Indica Intermediate  786 48.00% 8.70% 1.65% 41.73% NA
Temperate Japonica  767 1.20% 98.40% 0.00% 0.39% NA
Tropical Japonica  504 14.90% 82.70% 0.20% 2.18% NA
Japonica Intermediate  241 2.10% 97.50% 0.00% 0.41% NA
VI/Aromatic  96 6.20% 90.60% 0.00% 3.12% NA
Intermediate  90 37.80% 52.20% 1.11% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001243731 T -> C LOC_Os10g02990.1 missense_variant ; p.Gln545Arg; MODERATE nonsynonymous_codon ; Q545R Average:51.035; most accessible tissue: Callus, score: 93.142 unknown unknown TOLERATED 0.08
vg1001243731 T -> DEL LOC_Os10g02990.1 N frameshift_variant Average:51.035; most accessible tissue: Callus, score: 93.142 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001243731 9.42E-07 NA mr1486 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
vg1001243731 2.27E-10 6.93E-09 mr1486 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
vg1001243731 1.05E-06 1.54E-24 mr1548 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
vg1001243731 1.22E-09 1.45E-08 mr1548 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
vg1001243731 NA 8.36E-21 mr1588 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
vg1001243731 1.50E-07 2.54E-06 mr1588 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
vg1001243731 1.15E-06 4.90E-46 mr1486_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
vg1001243731 7.16E-11 1.39E-08 mr1486_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
vg1001243731 NA 7.53E-06 mr1530_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
vg1001243731 5.81E-07 4.01E-25 mr1588_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
vg1001243731 6.50E-12 3.48E-07 mr1588_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