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Detailed information for vg1000994377:

Variant ID: vg1000994377 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 994377
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:


TCTACTTTGATTTTGGATTCACTTTACACAAAACTGAAAACACATGAGATGAATATTCTTTCTCGTAAAATTGATTCTAATTCTAGTGCTTTGGTTTCTT[C/T]
CTCGACTTCTTTGGATGTTGGTGCTTCTTCATCAAATTCTACTGTTCTTGCTTTGATTAATGCCATGTCCGATGAGTAACTCGAACAGTTCGAGGAGGAC

Reverse complement sequence

GTCCTCCTCGAACTGTTCGAGTTACTCATCGGACATGGCATTAATCAAAGCAAGAACAGTAGAATTTGATGAAGAAGCACCAACATCCAAAGAAGTCGAG[G/A]
AAGAAACCAAAGCACTAGAATTAGAATCAATTTTACGAGAAAGAATATTCATCTCATGTGTTTTCAGTTTTGTGTAAAGTGAATCCAAAATCAAAGTAGA

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 92.00% 1.80% 2.98% 3.22% NA
All Indica  2759 86.80% 2.80% 4.93% 5.51% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 97.00% 1.90% 1.12% 0.00% NA
Indica I  595 82.90% 1.30% 9.41% 6.39% NA
Indica II  465 90.80% 2.60% 3.44% 3.23% NA
Indica III  913 84.10% 4.30% 3.50% 8.11% NA
Indica Intermediate  786 90.50% 2.30% 4.07% 3.18% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 1.11% 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
vg1000994377 C -> T LOC_Os10g02600.1 missense_variant ; p.Ser297Phe; MODERATE nonsynonymous_codon ; S297L Average:12.478; most accessible tissue: Callus, score: 33.393 unknown unknown DELETERIOUS 0.01
vg1000994377 C -> T LOC_Os10g02600.1 missense_variant ; p.Ser297Phe; MODERATE nonsynonymous_codon ; S297F Average:12.478; most accessible tissue: Callus, score: 33.393 unknown unknown DELETERIOUS 0.02
vg1000994377 C -> DEL LOC_Os10g02600.1 N frameshift_variant Average:12.478; most accessible tissue: Callus, score: 33.393 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000994377 9.54E-07 9.54E-07 mr1349 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