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Detailed information for vg0222778319:

Variant ID: vg0222778319 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22778319
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCCGAGAGGTCCGAGCTGTTCTCCCACAGCCCGAACCACCCCTTCCACTTCAACGTGCCGCACAGCTCGGCACCGATGGCTGGTATGCATCAGTGAGCC[A/G]
CGCCTCCAGGTTGCTGCAGCTAGCCCCAGGTACAACGAAGATCGGGTGGAGCTCGCCGGCGCCGACGCCGGCATCGTTTGGCCTGTGGTGGCTTGGCCAG

Reverse complement sequence

CTGGCCAAGCCACCACAGGCCAAACGATGCCGGCGTCGGCGCCGGCGAGCTCCACCCGATCTTCGTTGTACCTGGGGCTAGCTGCAGCAACCTGGAGGCG[T/C]
GGCTCACTGATGCATACCAGCCATCGGTGCCGAGCTGTGCGGCACGTTGAAGTGGAAGGGGTGGTTCGGGCTGTGGGAGAACAGCTCGGACCTCTCGGCG

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 44.10% 12.60% 1.40% 41.87% NA
All Indica  2759 31.00% 6.40% 1.88% 60.71% NA
All Japonica  1512 76.90% 20.90% 0.46% 1.72% NA
Aus  269 3.30% 1.50% 1.86% 93.31% NA
Indica I  595 12.90% 10.60% 2.02% 74.45% NA
Indica II  465 38.70% 0.20% 1.08% 60.00% NA
Indica III  913 36.70% 6.90% 2.08% 54.33% NA
Indica Intermediate  786 33.50% 6.40% 2.04% 58.14% NA
Temperate Japonica  767 92.40% 6.60% 0.65% 0.26% NA
Tropical Japonica  504 61.70% 33.70% 0.40% 4.17% NA
Japonica Intermediate  241 59.30% 39.40% 0.00% 1.24% NA
VI/Aromatic  96 7.30% 82.30% 1.04% 9.38% NA
Intermediate  90 55.60% 23.30% 1.11% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0222778319 A -> G LOC_Os02g37750.1 missense_variant ; p.Trp56Arg; MODERATE nonsynonymous_codon ; W56R Average:12.559; most accessible tissue: Callus, score: 72.278 benign -0.338 TOLERATED 1.00
vg0222778319 A -> DEL LOC_Os02g37750.1 N frameshift_variant Average:12.559; most accessible tissue: Callus, score: 72.278 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222778319 5.86E-06 NA mr1918 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
vg0222778319 2.80E-06 NA mr1067_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
vg0222778319 6.01E-08 NA mr1072_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
vg0222778319 1.34E-08 NA mr1075_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
vg0222778319 5.02E-07 NA mr1077_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
vg0222778319 2.32E-06 NA mr1124_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
vg0222778319 4.49E-07 NA mr1124_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
vg0222778319 2.14E-07 NA mr1149_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
vg0222778319 3.35E-07 NA mr1441_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
vg0222778319 2.36E-06 NA mr1918_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
vg0222778319 2.84E-06 NA mr1962_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