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Detailed information for vg1127357348:

Variant ID: vg1127357348 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27357348
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, T: 0.01, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


AATCGTCTGCCATGCTCCTTCTGGTACCGGCAAGGGTTGAAGTAACCCTGGATATTTGACTCTTTCTGGTTTGGCTTGAATGCAAACCTGGCAATGTTGA[A/T]
GCTGACATTTAACTTGCTTTTTCATTCCAGGCCAAGCAAACAATCTTTTAATTCTTCTATATGTGACAGGAAAACCCGAGTGCCCCCCAATGGGATTGTG

Reverse complement sequence

CACAATCCCATTGGGGGGCACTCGGGTTTTCCTGTCACATATAGAAGAATTAAAAGATTGTTTGCTTGGCCTGGAATGAAAAAGCAAGTTAAATGTCAGC[T/A]
TCAACATTGCCAGGTTTGCATTCAAGCCAAACCAGAAAGAGTCAAATATCCAGGGTTACTTCAACCCTTGCCGGTACCAGAAGGAGCATGGCAGACGATT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 48.80% 26.90% 1.10% 23.21% NA
All Indica  2759 48.10% 37.30% 1.05% 13.56% NA
All Japonica  1512 49.60% 9.90% 1.12% 39.42% NA
Aus  269 60.60% 2.60% 1.49% 35.32% NA
Indica I  595 69.70% 11.80% 1.51% 16.97% NA
Indica II  465 24.50% 72.50% 0.43% 2.58% NA
Indica III  913 49.60% 31.50% 1.20% 17.63% NA
Indica Intermediate  786 43.80% 42.60% 0.89% 12.72% NA
Temperate Japonica  767 66.60% 5.60% 0.52% 27.25% NA
Tropical Japonica  504 26.60% 11.50% 2.38% 59.52% NA
Japonica Intermediate  241 43.60% 19.90% 0.41% 36.10% NA
VI/Aromatic  96 26.00% 59.40% 1.04% 13.54% NA
Intermediate  90 45.60% 32.20% 1.11% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127357348 A -> T LOC_Os11g45190.1 downstream_gene_variant ; 2417.0bp to feature; MODIFIER silent_mutation Average:37.546; most accessible tissue: Minghui63 young leaf, score: 61.007 N N N N
vg1127357348 A -> T LOC_Os11g45210.1 downstream_gene_variant ; 4701.0bp to feature; MODIFIER silent_mutation Average:37.546; most accessible tissue: Minghui63 young leaf, score: 61.007 N N N N
vg1127357348 A -> T LOC_Os11g45200.1 intron_variant ; MODIFIER silent_mutation Average:37.546; most accessible tissue: Minghui63 young leaf, score: 61.007 N N N N
vg1127357348 A -> DEL N N silent_mutation Average:37.546; most accessible tissue: Minghui63 young leaf, score: 61.007 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127357348 NA 6.19E-11 mr1138 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
vg1127357348 NA 7.46E-06 mr1169 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
vg1127357348 NA 1.27E-08 mr1557 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
vg1127357348 7.95E-07 6.67E-06 mr1871 Jap_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
vg1127357348 NA 9.43E-06 mr1981 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
vg1127357348 NA 2.42E-06 mr1090_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
vg1127357348 NA 6.96E-06 mr1191_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
vg1127357348 NA 3.65E-07 mr1211_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
vg1127357348 NA 2.88E-07 mr1232_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
vg1127357348 NA 8.52E-09 mr1380_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
vg1127357348 NA 4.76E-09 mr1557_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
vg1127357348 NA 1.67E-08 mr1561_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
vg1127357348 NA 4.10E-09 mr1598_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
vg1127357348 NA 3.05E-06 mr1609_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
vg1127357348 NA 6.76E-08 mr1875_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
vg1127357348 NA 9.79E-06 mr1900_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
vg1127357348 NA 5.55E-07 mr1908_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
vg1127357348 NA 8.83E-07 mr1996_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