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Detailed information for vg0711119293:

Variant ID: vg0711119293 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 11119293
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


GACACAAAGTCCAGGATACAAATTAAATATACCTGGTCAAATCTGTGGTCAAGGAAATTAATCCATAGACAAATCAGCTATTACATGCACAAAGTGGTCT[C/T]
CAAACTAATCCATGCATGTGCTACCGACGATTACATGTCTACACGGCTGCATGACACGGCTGCATGCTACGGTTCATCCATTGACAGGCCTTGAATCAAA

Reverse complement sequence

TTTGATTCAAGGCCTGTCAATGGATGAACCGTAGCATGCAGCCGTGTCATGCAGCCGTGTAGACATGTAATCGTCGGTAGCACATGCATGGATTAGTTTG[G/A]
AGACCACTTTGTGCATGTAATAGCTGATTTGTCTATGGATTAATTTCCTTGACCACAGATTTGACCAGGTATATTTAATTTGTATCCTGGACTTTGTGTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.40% 5.50% 0.85% 6.22% NA
All Indica  2759 99.90% 0.00% 0.00% 0.04% NA
All Japonica  1512 61.40% 16.70% 2.51% 19.31% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.00% 0.13% NA
Temperate Japonica  767 75.10% 2.90% 1.83% 20.21% NA
Tropical Japonica  504 27.80% 43.70% 3.57% 25.00% NA
Japonica Intermediate  241 88.40% 4.60% 2.49% 4.56% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 8.90% 2.22% 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
vg0711119293 C -> DEL N N silent_mutation Average:38.373; most accessible tissue: Minghui63 flag leaf, score: 64.284 N N N N
vg0711119293 C -> T LOC_Os07g18790.1 upstream_gene_variant ; 363.0bp to feature; MODIFIER silent_mutation Average:38.373; most accessible tissue: Minghui63 flag leaf, score: 64.284 N N N N
vg0711119293 C -> T LOC_Os07g18780-LOC_Os07g18790 intergenic_region ; MODIFIER silent_mutation Average:38.373; most accessible tissue: Minghui63 flag leaf, score: 64.284 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0711119293 5.23E-06 NA mr1076 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
vg0711119293 NA 1.62E-06 mr1082 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
vg0711119293 NA 1.93E-09 mr1335_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
vg0711119293 7.09E-06 7.08E-06 mr1335_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
vg0711119293 3.12E-06 3.80E-11 mr1363_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
vg0711119293 NA 7.55E-09 mr1363_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
vg0711119293 NA 1.81E-07 mr1369_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
vg0711119293 NA 8.44E-07 mr1397_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
vg0711119293 NA 4.91E-08 mr1453_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
vg0711119293 NA 1.48E-06 mr1479_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
vg0711119293 NA 1.06E-07 mr1502_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
vg0711119293 NA 2.09E-08 mr1543_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
vg0711119293 NA 1.24E-07 mr1642_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
vg0711119293 NA 5.04E-13 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
vg0711119293 NA 1.79E-09 mr1825_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