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Detailed information for vg0524187250:

Variant ID: vg0524187250 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 24187250
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:


GCCCTTACCACCGACATTAGTAAAGCTCATAATTTCAGAAACAGGGTTCACTATTCTTCCAGAAGTCCATGTACCAAACTGTCAATTTTCATCATCATTA[G/A]
CATGTTTACAGATTCATCAGTGCCCAAATCTCATATCCTTACAGAATGGATTGCTTAGCCAGAAATTATTCTCTCTCCAGCAATTAACCATTACTAAGTG

Reverse complement sequence

CACTTAGTAATGGTTAATTGCTGGAGAGAGAATAATTTCTGGCTAAGCAATCCATTCTGTAAGGATATGAGATTTGGGCACTGATGAATCTGTAAACATG[C/T]
TAATGATGATGAAAATTGACAGTTTGGTACATGGACTTCTGGAAGAATAGTGAACCCTGTTTCTGAAATTATGAGCTTTACTAATGTCGGTGGTAAGGGC

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 51.50% 47.80% 0.06% 0.63% NA
All Indica  2759 29.80% 69.00% 0.11% 1.09% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 0.40% 99.60% 0.00% 0.00% NA
Indica I  595 41.20% 57.80% 0.00% 1.01% NA
Indica II  465 25.80% 73.10% 0.00% 1.08% NA
Indica III  913 27.70% 71.20% 0.00% 1.10% NA
Indica Intermediate  786 26.00% 72.50% 0.38% 1.15% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 61.50% 38.50% 0.00% 0.00% NA
Intermediate  90 54.40% 45.60% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0524187250 G -> DEL LOC_Os05g41290.1 N frameshift_variant Average:52.801; most accessible tissue: Callus, score: 77.615 N N N N
vg0524187250 G -> A LOC_Os05g41290.1 missense_variant ; p.Ala906Thr; MODERATE nonsynonymous_codon ; A906T Average:52.801; most accessible tissue: Callus, score: 77.615 unknown unknown TOLERATED 0.90

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0524187250 NA 9.01E-24 mr1168 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
vg0524187250 NA 4.19E-06 mr1291 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
vg0524187250 NA 5.99E-24 mr1383 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
vg0524187250 NA 2.71E-08 mr1806 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
vg0524187250 NA 9.67E-07 mr1153_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
vg0524187250 NA 6.05E-07 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
vg0524187250 NA 6.63E-21 mr1168_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
vg0524187250 NA 1.57E-06 mr1275_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
vg0524187250 NA 1.24E-17 mr1682_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
vg0524187250 NA 4.62E-06 mr1706_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
vg0524187250 NA 8.55E-14 mr1830_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
vg0524187250 NA 1.06E-13 mr1846_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
vg0524187250 NA 6.71E-06 mr1869_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
vg0524187250 NA 2.13E-07 mr1921_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
vg0524187250 NA 2.07E-06 mr1951_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
vg0524187250 NA 2.72E-11 mr1986_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