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Detailed information for vg0421220373:

Variant ID: vg0421220373 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 21220373
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTAAAATATGCCATCAGTATTCACGTATTTGAAACAATGCTATTACAATTTTACACAGATTCAAGATATGTCACTACCTACCATTTACAAAAAAAAAA[T/A]
TTAGATCAAATTACCCTTCTTTCCTTCTTTTTCTCCCCTCTCCTTCCTTCCACAGCTCAGAGAACAGGGGGCGGCGGTAGCAGCGAGCGGCAGCGTCGGA

Reverse complement sequence

TCCGACGCTGCCGCTCGCTGCTACCGCCGCCCCCTGTTCTCTGAGCTGTGGAAGGAAGGAGAGGGGAGAAAAAGAAGGAAAGAAGGGTAATTTGATCTAA[A/T]
TTTTTTTTTTGTAAATGGTAGGTAGTGACATATCTTGAATCTGTGTAAAATTGTAATAGCATTGTTTCAAATACGTGAATACTGATGGCATATTTTAAAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 39.00% 21.80% 4.95% 34.30% NA
All Indica  2759 8.40% 35.00% 7.36% 49.18% NA
All Japonica  1512 96.00% 1.70% 0.79% 1.52% NA
Aus  269 20.10% 8.60% 2.60% 68.77% NA
Indica I  595 12.40% 22.70% 15.46% 49.41% NA
Indica II  465 8.60% 27.70% 6.24% 57.42% NA
Indica III  913 3.80% 47.30% 2.30% 46.55% NA
Indica Intermediate  786 10.70% 34.40% 7.76% 47.20% NA
Temperate Japonica  767 98.70% 0.50% 0.78% 0.00% NA
Tropical Japonica  504 91.10% 4.00% 0.60% 4.37% NA
Japonica Intermediate  241 97.50% 0.80% 1.24% 0.41% NA
VI/Aromatic  96 50.00% 4.20% 3.12% 42.71% NA
Intermediate  90 62.20% 11.10% 10.00% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0421220373 T -> DEL N N silent_mutation Average:12.371; most accessible tissue: Callus, score: 46.936 N N N N
vg0421220373 T -> A LOC_Os04g34910.1 downstream_gene_variant ; 4388.0bp to feature; MODIFIER silent_mutation Average:12.371; most accessible tissue: Callus, score: 46.936 N N N N
vg0421220373 T -> A LOC_Os04g34910-LOC_Os04g34930 intergenic_region ; MODIFIER silent_mutation Average:12.371; most accessible tissue: Callus, score: 46.936 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0421220373 NA 1.60E-06 mr1192 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
vg0421220373 NA 2.24E-06 mr1627 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
vg0421220373 NA 1.95E-06 mr1158_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
vg0421220373 NA 5.54E-07 mr1158_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
vg0421220373 NA 3.79E-06 mr1184_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
vg0421220373 NA 7.27E-07 mr1277_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
vg0421220373 NA 3.31E-06 mr1312_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
vg0421220373 1.76E-06 1.76E-06 mr1312_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
vg0421220373 NA 8.92E-07 mr1378_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
vg0421220373 NA 5.74E-06 mr1417_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
vg0421220373 NA 1.86E-07 mr1641_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
vg0421220373 2.20E-06 2.19E-06 mr1651_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
vg0421220373 NA 3.58E-07 mr1653_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
vg0421220373 7.79E-06 7.79E-06 mr1665_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
vg0421220373 NA 9.16E-06 mr1682_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
vg0421220373 NA 8.69E-08 mr1683_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
vg0421220373 1.87E-06 1.87E-06 mr1687_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
vg0421220373 NA 4.94E-06 mr1738_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
vg0421220373 1.64E-06 1.64E-06 mr1738_2 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
vg0421220373 NA 6.99E-09 mr1759_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
vg0421220373 NA 4.13E-09 mr1759_2 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
vg0421220373 NA 2.20E-06 mr1766_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
vg0421220373 2.51E-06 2.51E-06 mr1812_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
vg0421220373 3.42E-06 3.42E-06 mr1816_2 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
vg0421220373 4.30E-06 4.30E-06 mr1832_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
vg0421220373 8.16E-07 8.16E-07 mr1833_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
vg0421220373 NA 6.45E-06 mr1838_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
vg0421220373 NA 3.68E-06 mr1856_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