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Detailed information for vg0432750231:

Variant ID: vg0432750231 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32750231
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.79, C: 0.21, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


TTGAATCACCATTCTACATACTATTTAAATTTAAATTATCATAAACCACATTAATTTACTTAATCTGGTGTTATCTAACTATCTTACATGTTTTTTTTTG[T/C]
TATCATACTAAATTTCCACAGCAATGCGCGGGATTTTACCTAGTATGTAATATATCAACGCACAAACTGTATCTTGTTAATTTCTTTTTTAAAAAATATA

Reverse complement sequence

TATATTTTTTAAAAAAGAAATTAACAAGATACAGTTTGTGCGTTGATATATTACATACTAGGTAAAATCCCGCGCATTGCTGTGGAAATTTAGTATGATA[A/G]
CAAAAAAAAACATGTAAGATAGTTAGATAACACCAGATTAAGTAAATTAATGTGGTTTATGATAATTTAAATTTAAATAGTATGTAGAATGGTGATTCAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 29.30% 6.20% 1.78% 62.72% NA
All Indica  2759 4.50% 0.20% 2.79% 92.53% NA
All Japonica  1512 72.80% 18.50% 0.07% 8.66% NA
Aus  269 36.80% 0.00% 0.74% 62.45% NA
Indica I  595 6.70% 0.50% 0.34% 92.44% NA
Indica II  465 2.80% 0.20% 0.43% 96.56% NA
Indica III  913 3.50% 0.00% 5.15% 91.35% NA
Indica Intermediate  786 5.00% 0.10% 3.31% 91.60% NA
Temperate Japonica  767 85.70% 13.40% 0.00% 0.91% NA
Tropical Japonica  504 69.60% 7.70% 0.20% 22.42% NA
Japonica Intermediate  241 38.20% 57.30% 0.00% 4.56% NA
VI/Aromatic  96 32.30% 0.00% 1.04% 66.67% NA
Intermediate  90 36.70% 6.70% 3.33% 53.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0432750231 T -> C LOC_Os04g55080.1 upstream_gene_variant ; 3434.0bp to feature; MODIFIER silent_mutation Average:52.763; most accessible tissue: Callus, score: 76.207 N N N N
vg0432750231 T -> C LOC_Os04g55060.1 downstream_gene_variant ; 3726.0bp to feature; MODIFIER silent_mutation Average:52.763; most accessible tissue: Callus, score: 76.207 N N N N
vg0432750231 T -> C LOC_Os04g55070.1 intron_variant ; MODIFIER silent_mutation Average:52.763; most accessible tissue: Callus, score: 76.207 N N N N
vg0432750231 T -> DEL N N silent_mutation Average:52.763; most accessible tissue: Callus, score: 76.207 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432750231 NA 6.39E-06 mr1113 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
vg0432750231 NA 1.74E-07 mr1114 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
vg0432750231 NA 3.19E-07 mr1116 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
vg0432750231 4.88E-06 NA mr1117 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
vg0432750231 NA 2.29E-09 mr1117 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
vg0432750231 NA 1.34E-06 mr1118 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
vg0432750231 NA 1.27E-07 mr1123 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
vg0432750231 NA 1.19E-07 mr1240 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
vg0432750231 NA 2.20E-06 mr1242 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
vg0432750231 1.21E-06 NA mr1247 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
vg0432750231 NA 2.83E-08 mr1247 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
vg0432750231 NA 4.54E-08 mr1496 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
vg0432750231 NA 1.53E-08 mr1691 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
vg0432750231 NA 4.05E-11 mr1693 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
vg0432750231 NA 5.81E-07 mr1693 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
vg0432750231 2.84E-06 NA mr1745 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
vg0432750231 NA 3.39E-06 mr1745 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
vg0432750231 3.12E-07 NA mr1917 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
vg0432750231 9.15E-07 3.57E-09 mr1917 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
vg0432750231 NA 4.03E-06 mr1961 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
vg0432750231 NA 4.48E-07 mr1114_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
vg0432750231 NA 1.38E-08 mr1117_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
vg0432750231 NA 1.39E-07 mr1119_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
vg0432750231 NA 2.16E-06 mr1120_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
vg0432750231 NA 4.48E-07 mr1240_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
vg0432750231 NA 2.10E-06 mr1242_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
vg0432750231 NA 5.76E-07 mr1247_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
vg0432750231 NA 6.19E-07 mr1496_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
vg0432750231 NA 7.01E-07 mr1691_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