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Detailed information for vg0618172241:

Variant ID: vg0618172241 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 18172241
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TGGTTGCGGTTGAGGATTACATTTCTTGCGGTTTTCTTCCTCCACCCTCCGAATTTCTTCTTCTCGTCTTGAACTTTTATGGCCTTTCCTTGCTTCACCT[A/G]
AACCCCAATTCCATCGCATTCCTCAGTATCTTCTCTTATCTTTGTGAGGCCTACATTGGGGTAGAGCCATTCCTTGATCTCTTCTGTTTTTACTACGAGT

Reverse complement sequence

ACTCGTAGTAAAAACAGAAGAGATCAAGGAATGGCTCTACCCCAATGTAGGCCTCACAAAGATAAGAGAAGATACTGAGGAATGCGATGGAATTGGGGTT[T/C]
AGGTGAAGCAAGGAAAGGCCATAAAAGTTCAAGACGAGAAGAAGAAATTCGGAGGGTGGAGGAAGAAAACCGCAAGAAATGTAATCCTCAACCGCAACCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.80% 29.00% 1.93% 8.25% NA
All Indica  2759 85.30% 13.80% 0.58% 0.25% NA
All Japonica  1512 8.50% 61.60% 4.76% 25.13% NA
Aus  269 89.60% 10.40% 0.00% 0.00% NA
Indica I  595 84.00% 13.80% 1.18% 1.01% NA
Indica II  465 95.30% 4.70% 0.00% 0.00% NA
Indica III  913 82.60% 17.20% 0.22% 0.00% NA
Indica Intermediate  786 83.60% 15.40% 0.89% 0.13% NA
Temperate Japonica  767 7.60% 54.60% 7.56% 30.25% NA
Tropical Japonica  504 10.70% 82.10% 0.79% 6.35% NA
Japonica Intermediate  241 7.10% 40.70% 4.15% 48.13% NA
VI/Aromatic  96 96.90% 2.10% 1.04% 0.00% NA
Intermediate  90 63.30% 31.10% 2.22% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0618172241 A -> G LOC_Os06g31240.1 synonymous_variant ; p.Leu77Leu; LOW synonymous_codon Average:50.857; most accessible tissue: Zhenshan97 flag leaf, score: 72.387 N N N N
vg0618172241 A -> DEL LOC_Os06g31240.1 N frameshift_variant Average:50.857; most accessible tissue: Zhenshan97 flag leaf, score: 72.387 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0618172241 NA 9.51E-06 mr1043 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
vg0618172241 NA 4.67E-06 mr1071 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
vg0618172241 NA 3.18E-12 mr1138 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
vg0618172241 NA 9.38E-06 mr1140 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
vg0618172241 NA 8.19E-13 mr1354 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
vg0618172241 NA 8.80E-06 mr1821 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
vg0618172241 NA 5.14E-06 mr1912 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
vg0618172241 NA 3.52E-07 mr1129_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
vg0618172241 NA 8.59E-12 mr1138_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
vg0618172241 NA 2.05E-07 mr1155_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
vg0618172241 NA 7.05E-06 mr1255_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
vg0618172241 NA 3.18E-06 mr1291_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
vg0618172241 NA 1.06E-12 mr1354_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