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Detailed information for vg0124212768:

Variant ID: vg0124212768 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 24212768
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.03, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GTCAATTGGATGATCCTTGGAAAGAGCGGTGTGTATCCTTAGTGGCATAGGTGGATCTTGTGCCTTCTCCTCCTCCACTTCAACTTGAGCTTGACTTGGC[G/A]
TAGCGGAAGTAGATGGCTCATCTTGAGTGGAGGTGGATGGCTTGTCTTCCACTTCAATAGGCTTGACATTTCCAATAGACATGTTCTTCATAGCTCTCAT

Reverse complement sequence

ATGAGAGCTATGAAGAACATGTCTATTGGAAATGTCAAGCCTATTGAAGTGGAAGACAAGCCATCCACCTCCACTCAAGATGAGCCATCTACTTCCGCTA[C/T]
GCCAAGTCAAGCTCAAGTTGAAGTGGAGGAGGAGAAGGCACAAGATCCACCTATGCCACTAAGGATACACACCGCTCTTTCCAAGGATCATCCAATTGAC

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 50.80% 48.80% 0.21% 0.13% NA
All Indica  2759 85.50% 14.10% 0.22% 0.14% NA
All Japonica  1512 0.50% 99.30% 0.07% 0.07% NA
Aus  269 0.00% 100.00% 0.00% 0.00% NA
Indica I  595 88.90% 10.80% 0.17% 0.17% NA
Indica II  465 95.50% 4.30% 0.00% 0.22% NA
Indica III  913 83.70% 16.00% 0.22% 0.11% NA
Indica Intermediate  786 79.30% 20.20% 0.38% 0.13% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.00% 0.00% 0.20% NA
Japonica Intermediate  241 1.20% 98.30% 0.41% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 36.70% 58.90% 3.33% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0124212768 G -> A LOC_Os01g42590.1 missense_variant ; p.Thr380Met; MODERATE nonsynonymous_codon ; T380M Average:31.303; most accessible tissue: Minghui63 panicle, score: 46.754 probably damaging 2.408 TOLERATED 0.16
vg0124212768 G -> DEL LOC_Os01g42590.1 N frameshift_variant Average:31.303; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0124212768 NA 2.81E-32 mr1026 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
vg0124212768 NA 5.85E-07 mr1220 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
vg0124212768 NA 3.48E-15 mr1261 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
vg0124212768 NA 2.28E-11 mr1609 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
vg0124212768 NA 1.36E-16 mr1870 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
vg0124212768 NA 4.39E-13 mr1883 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
vg0124212768 NA 5.28E-50 mr1063_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
vg0124212768 NA 9.82E-07 mr1346_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
vg0124212768 NA 8.67E-24 mr1422_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
vg0124212768 4.32E-06 NA mr1792_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
vg0124212768 NA 2.12E-06 mr1792_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
vg0124212768 NA 2.40E-06 mr1803_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
vg0124212768 NA 6.25E-07 mr1834_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
vg0124212768 NA 3.84E-20 mr1870_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
vg0124212768 NA 3.91E-29 mr1932_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