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Detailed information for vg1104144713:

Variant ID: vg1104144713 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 4144713
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTCAAGACATCGCTTTGCACTTTCCCCTTATGGAGTAAGGCATTCACAATGTCAGGCGAGCCGGCAACCACGGCGATGTGGAGCGGCGTGTTCCCAACC[C/T]
CGTCCTGCGCGTCCAGAAGGCCACCGACCTGCTTGTGTTTCTTGATAGCGAGGGACACGATCGAGGACTGCTTCTCCCTGACCGCGGTGTGCAGGAAGGT

Reverse complement sequence

ACCTTCCTGCACACCGCGGTCAGGGAGAAGCAGTCCTCGATCGTGTCCCTCGCTATCAAGAAACACAAGCAGGTCGGTGGCCTTCTGGACGCGCAGGACG[G/A]
GGTTGGGAACACGCCGCTCCACATCGCCGTGGTTGCCGGCTCGCCTGACATTGTGAATGCCTTACTCCATAAGGGGAAAGTGCAAAGCGATGTCTTGAAC

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 60.10% 38.80% 0.19% 0.83% NA
All Indica  2759 87.70% 10.90% 0.25% 1.09% NA
All Japonica  1512 11.20% 88.30% 0.07% 0.40% NA
Aus  269 40.50% 59.10% 0.00% 0.37% NA
Indica I  595 77.60% 19.50% 0.50% 2.35% NA
Indica II  465 93.10% 4.90% 0.43% 1.51% NA
Indica III  913 91.20% 8.50% 0.00% 0.22% NA
Indica Intermediate  786 88.20% 10.70% 0.25% 0.89% NA
Temperate Japonica  767 1.00% 99.00% 0.00% 0.00% NA
Tropical Japonica  504 28.40% 70.20% 0.20% 1.19% NA
Japonica Intermediate  241 7.90% 92.10% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 57.80% 38.90% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1104144713 C -> T LOC_Os11g07970.1 upstream_gene_variant ; 4234.0bp to feature; MODIFIER silent_mutation Average:58.217; most accessible tissue: Callus, score: 81.544 N N N N
vg1104144713 C -> T LOC_Os11g07970-LOC_Os11g07980 intergenic_region ; MODIFIER silent_mutation Average:58.217; most accessible tissue: Callus, score: 81.544 N N N N
vg1104144713 C -> DEL N N silent_mutation Average:58.217; most accessible tissue: Callus, score: 81.544 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1104144713 NA 1.40E-06 mr1027 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
vg1104144713 NA 1.38E-08 mr1174 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
vg1104144713 NA 4.51E-06 mr1180 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
vg1104144713 4.05E-11 3.96E-13 mr1218 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
vg1104144713 NA 8.49E-08 mr1422 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
vg1104144713 NA 4.95E-06 mr1503 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
vg1104144713 NA 1.69E-08 mr1583 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
vg1104144713 8.40E-07 3.02E-08 mr1638 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
vg1104144713 NA 1.02E-06 mr1794 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
vg1104144713 2.91E-08 5.07E-11 mr1218_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
vg1104144713 1.58E-07 1.67E-11 mr1850_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