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Detailed information for vg0138783722:

Variant ID: vg0138783722 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 38783722
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TGGCGAAAAGAAGATTGATTGAGCTGCCACCGTCGATGAGGACTCGCGCTACTTTGATGTTCCGAATAGTGGGTTCGACCATGATCGGATATCGTCCTGG[G/C]
ATGACGGCGGTCTTGGGGTGGTCTTCTTCCGAGAACTCTATCTTCTGCTCATACCACTTCATCTTGGGTGCAGCCCCCTGCCATGTCGAACAGACTTCAC

Reverse complement sequence

GTGAAGTCTGTTCGACATGGCAGGGGGCTGCACCCAAGATGAAGTGGTATGAGCAGAAGATAGAGTTCTCGGAAGAAGACCACCCCAAGACCGCCGTCAT[C/G]
CCAGGACGATATCCGATCATGGTCGAACCCACTATTCGGAACATCAAAGTAGCGCGAGTCCTCATCGACGGTGGCAGCTCAATCAATCTTCTTTTCGCCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.00% 19.60% 0.44% 0.00% NA
All Indica  2759 66.50% 32.80% 0.76% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 47.10% 51.90% 1.01% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 57.00% 42.30% 0.77% 0.00% NA
Indica Intermediate  786 74.00% 24.90% 1.02% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0138783722 G -> C LOC_Os01g66790.1 missense_variant ; p.Ile659Met; MODERATE nonsynonymous_codon ; I659M Average:41.1; most accessible tissue: Minghui63 flag leaf, score: 59.244 probably damaging 2.525 TOLERATED 0.14

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0138783722 4.52E-06 4.52E-06 mr1834 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
vg0138783722 NA 8.61E-06 mr1265_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