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Detailed information for vg0515732737:

Variant ID: vg0515732737 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 15732737
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTTTCAATTGGTATCAGAGCCCGGTTAAGTTCGTTGTAACCTAACCGTGGCAACGAACGCAGCTATGGAGGAAAAATACTCTATGAAACCATTTGTTTT[C/T]
GATGGACACAATTTTGTCATTTGGAAGGCACGAATGGAGGCCTACCTCCCGTCGCAAGGGCATAATGTGTGGAATAAGGTTAAATCACCTTACACTGTGC

Reverse complement sequence

GCACAGTGTAAGGTGATTTAACCTTATTCCACACATTATGCCCTTGCGACGGGAGGTAGGCCTCCATTCGTGCCTTCCAAATGACAAAATTGTGTCCATC[G/A]
AAAACAAATGGTTTCATAGAGTATTTTTCCTCCATAGCTGCGTTCGTTGCCACGGTTAGGTTACAACGAACTTAACCGGGCTCTGATACCAATTGAAAGA

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 66.50% 16.60% 4.25% 12.67% NA
All Indica  2759 96.70% 1.40% 0.69% 1.16% NA
All Japonica  1512 5.40% 47.80% 10.25% 36.57% NA
Aus  269 92.20% 0.70% 7.06% 0.00% NA
Indica I  595 94.60% 3.40% 1.34% 0.67% NA
Indica II  465 95.10% 1.70% 0.65% 2.58% NA
Indica III  913 98.60% 0.50% 0.44% 0.44% NA
Indica Intermediate  786 97.20% 0.80% 0.51% 1.53% NA
Temperate Japonica  767 2.70% 82.80% 1.96% 12.52% NA
Tropical Japonica  504 7.10% 6.50% 18.25% 68.06% NA
Japonica Intermediate  241 10.00% 22.80% 19.92% 47.30% NA
VI/Aromatic  96 82.30% 2.10% 6.25% 9.38% NA
Intermediate  90 71.10% 21.10% 2.22% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0515732737 C -> T LOC_Os05g27060.1 synonymous_variant ; p.Phe12Phe; LOW synonymous_codon Average:8.375; most accessible tissue: Callus, score: 15.811 N N N N
vg0515732737 C -> DEL LOC_Os05g27060.1 N frameshift_variant Average:8.375; most accessible tissue: Callus, score: 15.811 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0515732737 NA 1.18E-14 Grain_thickness Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0515732737 NA 3.57E-10 mr1235 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
vg0515732737 NA 5.70E-08 mr1243 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
vg0515732737 NA 8.10E-07 mr1415 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
vg0515732737 NA 1.03E-07 mr1423 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
vg0515732737 NA 8.75E-06 mr1555 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
vg0515732737 NA 8.10E-07 mr1567 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
vg0515732737 NA 4.43E-10 mr1087_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
vg0515732737 NA 6.13E-11 mr1089_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
vg0515732737 NA 4.96E-06 mr1091_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
vg0515732737 NA 1.62E-10 mr1093_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
vg0515732737 NA 7.01E-12 mr1235_2 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
vg0515732737 NA 5.64E-07 mr1243_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
vg0515732737 NA 6.51E-09 mr1251_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
vg0515732737 NA 1.82E-06 mr1257_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
vg0515732737 NA 3.58E-08 mr1423_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
vg0515732737 NA 6.95E-09 mr1435_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
vg0515732737 NA 3.30E-10 mr1599_2 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
vg0515732737 NA 5.31E-08 mr1805_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
vg0515732737 NA 1.64E-08 mr1862_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
vg0515732737 NA 2.51E-07 mr1991_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