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Detailed information for vg1003043919:

Variant ID: vg1003043919 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3043919
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.69, C: 0.31, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


GAAGGGAAAATGACGAGTAGAAGACATGTATTTGGGTAGTTCCATAATGCACACAGTAGAAATCATTTGTCAGAATCAGTGTTTTGGCAGAAAAGGTAGA[A/C]
GAACGCAGAGTACTCTGCATTTTGTAATATAGGCATTGGACTAGCATAGAATATTAGAATCGATAGTCTCAGGATTGGTGATTGCATTAGTACATTGGAA

Reverse complement sequence

TTCCAATGTACTAATGCAATCACCAATCCTGAGACTATCGATTCTAATATTCTATGCTAGTCCAATGCCTATATTACAAAATGCAGAGTACTCTGCGTTC[T/G]
TCTACCTTTTCTGCCAAAACACTGATTCTGACAAATGATTTCTACTGTGTGCATTATGGAACTACCCAAATACATGTCTTCTACTCGTCATTTTCCCTTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.90% 28.00% 0.04% 0.00% NA
All Indica  2759 67.40% 32.60% 0.04% 0.00% NA
All Japonica  1512 76.30% 23.70% 0.00% 0.00% NA
Aus  269 96.70% 3.30% 0.00% 0.00% NA
Indica I  595 65.00% 34.80% 0.17% 0.00% NA
Indica II  465 69.20% 30.80% 0.00% 0.00% NA
Indica III  913 75.70% 24.30% 0.00% 0.00% NA
Indica Intermediate  786 58.40% 41.60% 0.00% 0.00% NA
Temperate Japonica  767 62.30% 37.70% 0.00% 0.00% NA
Tropical Japonica  504 95.80% 4.20% 0.00% 0.00% NA
Japonica Intermediate  241 79.70% 20.30% 0.00% 0.00% NA
VI/Aromatic  96 58.30% 40.60% 1.04% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg1003043919 A -> C LOC_Os10g06010.1 downstream_gene_variant ; 2551.0bp to feature; MODIFIER silent_mutation Average:59.61; most accessible tissue: Minghui63 root, score: 70.332 N N N N
vg1003043919 A -> C LOC_Os10g06000-LOC_Os10g06010 intergenic_region ; MODIFIER silent_mutation Average:59.61; most accessible tissue: Minghui63 root, score: 70.332 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003043919 NA 2.33E-07 mr1062 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
vg1003043919 NA 6.43E-06 mr1210 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
vg1003043919 NA 6.87E-06 mr1305 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
vg1003043919 1.56E-07 7.87E-09 mr1547 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
vg1003043919 NA 4.11E-06 mr1547 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
vg1003043919 NA 1.08E-07 mr1585 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
vg1003043919 NA 4.94E-06 mr1586 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
vg1003043919 5.96E-09 2.70E-15 mr1709 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
vg1003043919 6.29E-08 1.84E-12 mr1709 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
vg1003043919 NA 9.60E-06 mr1922 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
vg1003043919 NA 6.31E-07 mr1062_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
vg1003043919 NA 6.20E-06 mr1167_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
vg1003043919 NA 9.62E-08 mr1547_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
vg1003043919 NA 3.79E-06 mr1547_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
vg1003043919 NA 2.76E-06 mr1585_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
vg1003043919 1.48E-17 9.93E-30 mr1709_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
vg1003043919 4.08E-14 4.06E-21 mr1709_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
vg1003043919 6.36E-06 1.50E-13 mr1709_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