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Detailed information for vg0603711280:

Variant ID: vg0603711280 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 3711280
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAACATTATCGAAACTTTAGTTTGCCCTGAATCTGAGACAAAATTTCTGAACAAACAATAATCTTACCTTTCAACAATATAAGTGCCCGCGCATACGCGT[G/C]
GGCCACCTTACTAGTTTTACACTAAATTTTTGATACCTCATGGTATCTCCTCAAGGACCATAGAATTGCTCAAAGACTTCATGTCATGGAAAACTAAAGC

Reverse complement sequence

GCTTTAGTTTTCCATGACATGAAGTCTTTGAGCAATTCTATGGTCCTTGAGGAGATACCATGAGGTATCAAAAATTTAGTGTAAAACTAGTAAGGTGGCC[C/G]
ACGCGTATGCGCGGGCACTTATATTGTTGAAAGGTAAGATTATTGTTTGTTCAGAAATTTTGTCTCAGATTCAGGGCAAACTAAAGTTTCGATAATGTTA

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 88.80% 11.20% 0.02% 0.00% NA
All Indica  2759 87.80% 12.20% 0.04% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 32.00% 68.00% 0.00% 0.00% NA
Indica I  595 77.50% 22.40% 0.17% 0.00% NA
Indica II  465 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 77.40% 22.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0603711280 G -> C LOC_Os06g07670.1 upstream_gene_variant ; 2575.0bp to feature; MODIFIER silent_mutation Average:35.109; most accessible tissue: Zhenshan97 flag leaf, score: 49.845 N N N N
vg0603711280 G -> C LOC_Os06g07660.1 intron_variant ; MODIFIER silent_mutation Average:35.109; most accessible tissue: Zhenshan97 flag leaf, score: 49.845 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0603711280 NA 2.43E-08 mr1184 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
vg0603711280 NA 6.93E-06 mr1209 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
vg0603711280 NA 1.54E-07 mr1629 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
vg0603711280 NA 1.19E-08 mr1629_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