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Detailed information for vg1004292753:

Variant ID: vg1004292753 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4292753
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, A: 0.22, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


CTTACTTTATTATCCAAAGTACTTTAAGCATAACTTTTCGTTTTTTATATTTACACAAATTTTTTAAATAAGATGAGTGGTCAAACAGTGGAAGCAAAAT[G/A]
TCAAAATCCCTTATATTATGGGACGGAGGGAGTATATTTTATTATAGTGTAATTACATACATACAAGCGGGAAAGGAAAAAAAATCAAAGCGCGTGCATG

Reverse complement sequence

CATGCACGCGCTTTGATTTTTTTTCCTTTCCCGCTTGTATGTATGTAATTACACTATAATAAAATATACTCCCTCCGTCCCATAATATAAGGGATTTTGA[C/T]
ATTTTGCTTCCACTGTTTGACCACTCATCTTATTTAAAAAATTTGTGTAAATATAAAAAACGAAAAGTTATGCTTAAAGTACTTTGGATAATAAAGTAAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.60% 46.10% 0.32% 0.00% NA
All Indica  2759 60.80% 38.70% 0.47% 0.00% NA
All Japonica  1512 48.20% 51.70% 0.07% 0.00% NA
Aus  269 2.60% 97.40% 0.00% 0.00% NA
Indica I  595 39.30% 60.20% 0.50% 0.00% NA
Indica II  465 63.40% 35.70% 0.86% 0.00% NA
Indica III  913 78.30% 21.40% 0.33% 0.00% NA
Indica Intermediate  786 55.20% 44.40% 0.38% 0.00% NA
Temperate Japonica  767 12.40% 87.50% 0.13% 0.00% NA
Tropical Japonica  504 94.20% 5.80% 0.00% 0.00% NA
Japonica Intermediate  241 66.00% 34.00% 0.00% 0.00% NA
VI/Aromatic  96 63.50% 36.50% 0.00% 0.00% NA
Intermediate  90 65.60% 33.30% 1.11% 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
vg1004292753 G -> A LOC_Os10g07998.1 intron_variant ; MODIFIER silent_mutation Average:50.491; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004292753 NA 9.44E-07 mr1206 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
vg1004292753 NA 4.58E-06 mr1300 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
vg1004292753 NA 2.75E-06 mr1308 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
vg1004292753 NA 1.46E-07 mr1310 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
vg1004292753 NA 8.72E-06 mr1317 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
vg1004292753 4.72E-06 2.50E-12 mr1603 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
vg1004292753 2.96E-06 1.12E-07 mr1603 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
vg1004292753 NA 5.43E-06 mr1308_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
vg1004292753 NA 1.58E-07 mr1310_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
vg1004292753 NA 1.40E-06 mr1361_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
vg1004292753 NA 5.14E-07 mr1603_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