Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0619177386:

Variant ID: vg0619177386 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19177386
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGAACAATGTTACTATTACTTTGTCGGATGAAGAAATGACCGAAATAAAAGTTTTAGATTTTGATGAGTTATTCATCTTTGTTGTTGATAACTTTTTCA[G/A]
TTGAAATCATTTAGTATTTGAAAATATTGTTTGAAGTTGTCATATTTTTAAATTTAAATTCGAACAGTTCAAAAAATGTTATATAGAAAAATGGCCAAAA

Reverse complement sequence

TTTTGGCCATTTTTCTATATAACATTTTTTGAACTGTTCGAATTTAAATTTAAAAATATGACAACTTCAAACAATATTTTCAAATACTAAATGATTTCAA[C/T]
TGAAAAAGTTATCAACAACAAAGATGAATAACTCATCAAAATCTAAAACTTTTATTTCGGTCATTTCTTCATCCGACAAAGTAATAGTAACATTGTTCAC

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 87.50% 6.10% 0.95% 5.50% NA
All Indica  2759 98.60% 0.80% 0.18% 0.36% NA
All Japonica  1512 64.00% 17.20% 2.58% 16.27% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.30% 0.00% 0.17% 1.51% NA
Indica II  465 98.30% 1.30% 0.43% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 1.70% 0.25% 0.13% NA
Temperate Japonica  767 73.00% 0.40% 2.74% 23.86% NA
Tropical Japonica  504 45.80% 48.20% 2.78% 3.17% NA
Japonica Intermediate  241 73.00% 5.80% 1.66% 19.50% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 91.10% 4.40% 1.11% 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
vg0619177386 G -> A LOC_Os06g32920-LOC_Os06g32944 intergenic_region ; MODIFIER silent_mutation Average:13.821; most accessible tissue: Zhenshan97 young leaf, score: 19.578 N N N N
vg0619177386 G -> DEL N N silent_mutation Average:13.821; most accessible tissue: Zhenshan97 young leaf, score: 19.578 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619177386 NA 7.29E-07 mr1993 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
vg0619177386 4.66E-06 NA mr1083_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
vg0619177386 3.31E-06 NA mr1085_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
vg0619177386 NA 7.78E-07 mr1217_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
vg0619177386 NA 7.39E-07 mr1218_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
vg0619177386 NA 3.47E-09 mr1408_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
vg0619177386 NA 1.12E-08 mr1696_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
vg0619177386 1.29E-06 NA mr1800_2 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
vg0619177386 2.48E-06 NA mr1850_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
vg0619177386 NA 1.49E-06 mr1850_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