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Detailed information for vg0113613619:

Variant ID: vg0113613619 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13613619
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACCCCGTCAGCCTGGTATTGATATTGACGTATTTCTTGAACCATTGTTGGAAGATATGGCTGATTTATGGAAAGAGGGATTGAAAATGTGGGACGAGTA[C/T]
TTAAGAGAATACTTCACAGTGAAGGCCATCATCTTCGTGACCATTAACGATTATCCAGCAATGTTTTCAGTTTCAGGTCAAATTAAAGGTAAAAACAGGA

Reverse complement sequence

TCCTGTTTTTACCTTTAATTTGACCTGAAACTGAAAACATTGCTGGATAATCGTTAATGGTCACGAAGATGATGGCCTTCACTGTGAAGTATTCTCTTAA[G/A]
TACTCGTCCCACATTTTCAATCCCTCTTTCCATAAATCAGCCATATCTTCCAACAATGGTTCAAGAAATACGTCAATATCAATACCAGGCTGACGGGGTC

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 54.00% 0.80% 7.70% 37.54% NA
All Indica  2759 39.20% 0.70% 9.53% 50.63% NA
All Japonica  1512 87.50% 0.20% 2.58% 9.72% NA
Aus  269 20.80% 0.40% 13.38% 65.43% NA
Indica I  595 58.80% 0.30% 3.19% 37.65% NA
Indica II  465 26.90% 0.00% 7.31% 65.81% NA
Indica III  913 33.10% 1.50% 14.57% 50.82% NA
Indica Intermediate  786 38.70% 0.30% 9.80% 51.27% NA
Temperate Japonica  767 98.80% 0.00% 0.26% 0.91% NA
Tropical Japonica  504 67.50% 0.60% 6.75% 25.20% NA
Japonica Intermediate  241 93.40% 0.00% 1.24% 5.39% NA
VI/Aromatic  96 39.60% 15.60% 20.83% 23.96% NA
Intermediate  90 57.80% 1.10% 6.67% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0113613619 C -> T LOC_Os01g24140.1 synonymous_variant ; p.Tyr377Tyr; LOW synonymous_codon Average:21.738; most accessible tissue: Zhenshan97 root, score: 53.045 N N N N
vg0113613619 C -> DEL LOC_Os01g24140.1 N frameshift_variant Average:21.738; most accessible tissue: Zhenshan97 root, score: 53.045 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113613619 1.15E-07 NA mr1168 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
vg0113613619 9.43E-10 NA mr1383 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
vg0113613619 1.05E-07 2.04E-06 mr1383 Ind_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