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Detailed information for vg0221844814:

Variant ID: vg0221844814 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21844814
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTACGTACTGTTGCAAAATTGATAAATATATGGTTAATTGTATTTAATTTGTTACTACTAAATATTAGTAATGCATAGGGAAATTTGGCACAGCATATTT[G/A]
TTCCATCCTACTGAAATTTGACAATTCTACCAAATCTACCGAAAATTTGGTATTGCTAAATTTTTTTGAACAGAAATATTGTCAAATTTTGGTGAACATG

Reverse complement sequence

CATGTTCACCAAAATTTGACAATATTTCTGTTCAAAAAAATTTAGCAATACCAAATTTTCGGTAGATTTGGTAGAATTGTCAAATTTCAGTAGGATGGAA[C/T]
AAATATGCTGTGCCAAATTTCCCTATGCATTACTAATATTTAGTAGTAACAAATTAAATACAATTAACCATATATTTATCAATTTTGCAACAGTACGTAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 77.00% 8.40% 5.35% 9.27% NA
All Indica  2759 98.90% 0.40% 0.22% 0.40% NA
All Japonica  1512 37.30% 22.50% 15.34% 24.87% NA
Aus  269 99.60% 0.00% 0.00% 0.37% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 98.80% 0.30% 0.22% 0.66% NA
Indica Intermediate  786 98.10% 0.80% 0.51% 0.64% NA
Temperate Japonica  767 54.40% 11.20% 15.38% 19.04% NA
Tropical Japonica  504 21.80% 32.90% 14.48% 30.75% NA
Japonica Intermediate  241 15.40% 36.50% 17.01% 31.12% NA
VI/Aromatic  96 14.60% 36.50% 11.46% 37.50% NA
Intermediate  90 67.80% 12.20% 4.44% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0221844814 G -> A LOC_Os02g36210.1 intron_variant ; MODIFIER silent_mutation Average:50.864; most accessible tissue: Callus, score: 68.704 N N N N
vg0221844814 G -> DEL N N silent_mutation Average:50.864; most accessible tissue: Callus, score: 68.704 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0221844814 NA 3.89E-10 mr1097 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
vg0221844814 NA 3.51E-10 mr1128 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
vg0221844814 4.90E-06 1.06E-19 mr1042_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
vg0221844814 NA 2.29E-06 mr1184_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
vg0221844814 1.67E-07 1.67E-07 mr1186_2 Jap_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
vg0221844814 4.42E-06 4.42E-06 mr1245_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
vg0221844814 NA 1.59E-06 mr1278_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
vg0221844814 1.10E-06 NA mr1305_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
vg0221844814 NA 3.07E-06 mr1329_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
vg0221844814 NA 4.51E-11 mr1379_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
vg0221844814 NA 5.41E-08 mr1554_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
vg0221844814 NA 8.94E-10 mr1559_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
vg0221844814 NA 7.13E-06 mr1559_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
vg0221844814 1.04E-08 NA mr1585_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
vg0221844814 5.19E-07 5.19E-07 mr1647_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
vg0221844814 2.79E-06 NA mr1648_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
vg0221844814 9.65E-06 NA mr1742_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
vg0221844814 NA 5.40E-09 mr1851_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
vg0221844814 NA 1.36E-11 mr1947_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
vg0221844814 NA 9.65E-07 mr1977_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