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Detailed information for vg0142373682:

Variant ID: vg0142373682 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 42373682
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACATTCAATGAAACTAATTTCATGCTAAGTTTGTCTGTGAACATGGTTAACTATATTTAAAAAAAACTGGCTTAGAAAAAAAACAATGCATCTATAATAT[C/A]
AAACGGAGGTTATAAAATCCCATCCTTCTATATATATAATCCTTCATATATATCCTGATCTTGCCGAGATGGCTAGCTGATATATTATGACTAATTAAGT

Reverse complement sequence

ACTTAATTAGTCATAATATATCAGCTAGCCATCTCGGCAAGATCAGGATATATATGAAGGATTATATATATAGAAGGATGGGATTTTATAACCTCCGTTT[G/T]
ATATTATAGATGCATTGTTTTTTTTCTAAGCCAGTTTTTTTTAAATATAGTTAACCATGTTCACAGACAAACTTAGCATGAAATTAGTTTCATTGAATGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.90% 8.60% 0.44% 15.04% NA
All Indica  2759 79.90% 0.30% 0.62% 19.14% NA
All Japonica  1512 68.10% 24.00% 0.00% 7.94% NA
Aus  269 78.80% 2.60% 0.74% 17.84% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 31.40% 0.00% 1.51% 67.10% NA
Indica III  913 88.80% 0.30% 0.44% 10.41% NA
Indica Intermediate  786 83.10% 0.80% 0.76% 15.39% NA
Temperate Japonica  767 80.70% 18.90% 0.00% 0.39% NA
Tropical Japonica  504 54.20% 23.60% 0.00% 22.22% NA
Japonica Intermediate  241 56.80% 41.10% 0.00% 2.07% NA
VI/Aromatic  96 77.10% 19.80% 0.00% 3.12% NA
Intermediate  90 75.60% 8.90% 2.22% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0142373682 C -> A LOC_Os01g73040.1 upstream_gene_variant ; 3512.0bp to feature; MODIFIER silent_mutation Average:36.523; most accessible tissue: Callus, score: 80.51 N N N N
vg0142373682 C -> A LOC_Os01g73024.1 downstream_gene_variant ; 3317.0bp to feature; MODIFIER silent_mutation Average:36.523; most accessible tissue: Callus, score: 80.51 N N N N
vg0142373682 C -> A LOC_Os01g73024-LOC_Os01g73040 intergenic_region ; MODIFIER silent_mutation Average:36.523; most accessible tissue: Callus, score: 80.51 N N N N
vg0142373682 C -> DEL N N silent_mutation Average:36.523; most accessible tissue: Callus, score: 80.51 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0142373682 NA 4.80E-16 Grain_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0142373682 NA 5.70E-12 Grain_width Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0142373682 NA 6.12E-07 mr1502 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
vg0142373682 NA 2.84E-06 mr1543 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
vg0142373682 NA 5.80E-06 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
vg0142373682 NA 9.74E-07 mr1919 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
vg0142373682 NA 3.77E-08 mr1919 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
vg0142373682 NA 8.75E-07 mr1928 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
vg0142373682 NA 2.08E-07 mr1931 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
vg0142373682 NA 4.77E-06 mr1942 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
vg0142373682 2.94E-06 2.27E-12 mr1974 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
vg0142373682 1.65E-06 2.04E-13 mr1974 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
vg0142373682 NA 2.74E-06 mr1984 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
vg0142373682 NA 2.68E-08 mr1188_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
vg0142373682 NA 8.44E-06 mr1319_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
vg0142373682 NA 1.10E-07 mr1322_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
vg0142373682 NA 8.83E-08 mr1323_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
vg0142373682 NA 1.19E-09 mr1330_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
vg0142373682 NA 1.20E-06 mr1332_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
vg0142373682 NA 1.50E-07 mr1336_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
vg0142373682 NA 4.99E-06 mr1438_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
vg0142373682 NA 7.26E-06 mr1527_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
vg0142373682 NA 9.49E-07 mr1540_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
vg0142373682 NA 7.63E-08 mr1557_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
vg0142373682 NA 5.23E-06 mr1579_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
vg0142373682 NA 1.01E-06 mr1732_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
vg0142373682 NA 3.24E-10 mr1928_2 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
vg0142373682 NA 4.04E-07 mr1928_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
vg0142373682 NA 1.10E-09 mr1931_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
vg0142373682 NA 1.07E-06 mr1931_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
vg0142373682 NA 1.11E-06 mr1942_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
vg0142373682 3.15E-06 8.50E-09 mr1974_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
vg0142373682 1.01E-06 2.89E-10 mr1974_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