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Detailed information for vg1000628134:

Variant ID: vg1000628134 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 628134
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


GGCCAATCGTTGATGGTTACGAACAGCAGCGCTAGTAGGTTAAATTCCTCCTGTTTGTCTTCGTCCCACACGGGGACACCTTCCTTCTTCCATAATAGTT[T/C]
AAGATCTTCGACCAGTGGTCTTAGGAACACATCGATGTCGTTACCAGGTTGCTTGGGGCCTTGAATAATAATCGGCATCATTATGTACTTCCTCTTCATG

Reverse complement sequence

CATGAAGAGGAAGTACATAATGATGCCGATTATTATTCAAGGCCCCAAGCAACCTGGTAACGACATCGATGTGTTCCTAAGACCACTGGTCGAAGATCTT[A/G]
AACTATTATGGAAGAAGGAAGGTGTCCCCGTGTGGGACGAAGACAAACAGGAGGAATTTAACCTACTAGCGCTGCTGTTCGTAACCATCAACGATTGGCC

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 93.70% 3.20% 2.01% 1.14% NA
All Indica  2759 98.70% 0.00% 1.30% 0.00% NA
All Japonica  1512 86.00% 9.40% 1.12% 3.51% NA
Aus  269 94.40% 1.90% 3.72% 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 96.50% 0.00% 3.50% 0.00% NA
Indica Intermediate  786 99.40% 0.10% 0.51% 0.00% NA
Temperate Japonica  767 86.60% 5.60% 1.30% 6.52% NA
Tropical Japonica  504 96.00% 4.00% 0.00% 0.00% NA
Japonica Intermediate  241 63.10% 32.80% 2.90% 1.24% NA
VI/Aromatic  96 68.80% 0.00% 30.21% 1.04% NA
Intermediate  90 95.60% 1.10% 3.33% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1000628134 T -> C LOC_Os10g01984.1 missense_variant ; p.Lys387Glu; MODERATE nonsynonymous_codon ; K387E Average:24.107; most accessible tissue: Zhenshan97 panicle, score: 36.038 benign 0.846 DELETERIOUS 0.00
vg1000628134 T -> DEL LOC_Os10g01984.1 N frameshift_variant Average:24.107; most accessible tissue: Zhenshan97 panicle, score: 36.038 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000628134 3.35E-06 8.16E-09 mr1719 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
vg1000628134 NA 5.36E-06 mr1113_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