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Detailed information for vg1005627516:

Variant ID: vg1005627516 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5627516
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


TTGTGAGGGGAGAGTCCGACTCTCCACTTCATCTGTAGGCCGAACCTACCAACTCCTCTCCATAAGGCCTGGTTTAGTTCCCAACTTTTTCTTCAAACTT[C/T]
CAACTTTTCCATCACATCAAAACTTTCCTACACACACAAACTTTCAACTTTTCCGTCACATCGTTCCAATTTCAATCAAACTTTCAATTTTGGCGTGAAC

Reverse complement sequence

GTTCACGCCAAAATTGAAAGTTTGATTGAAATTGGAACGATGTGACGGAAAAGTTGAAAGTTTGTGTGTGTAGGAAAGTTTTGATGTGATGGAAAAGTTG[G/A]
AAGTTTGAAGAAAAAGTTGGGAACTAAACCAGGCCTTATGGAGAGGAGTTGGTAGGTTCGGCCTACAGATGAAGTGGAGAGTCGGACTCTCCCCTCACAA

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 82.80% 17.20% 0.02% 0.00% NA
All Indica  2759 81.10% 18.90% 0.00% 0.00% NA
All Japonica  1512 81.30% 18.70% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 79.10% 20.90% 0.00% 0.00% NA
Indica III  913 70.00% 30.00% 0.00% 0.00% NA
Indica Intermediate  786 81.20% 18.80% 0.00% 0.00% NA
Temperate Japonica  767 89.80% 10.00% 0.13% 0.00% NA
Tropical Japonica  504 76.40% 23.60% 0.00% 0.00% NA
Japonica Intermediate  241 64.30% 35.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 0.00% 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
vg1005627516 C -> T LOC_Os10g10214.1 upstream_gene_variant ; 4641.0bp to feature; MODIFIER silent_mutation Average:46.434; most accessible tissue: Callus, score: 62.407 N N N N
vg1005627516 C -> T LOC_Os10g10244.1 upstream_gene_variant ; 4731.0bp to feature; MODIFIER silent_mutation Average:46.434; most accessible tissue: Callus, score: 62.407 N N N N
vg1005627516 C -> T LOC_Os10g10230.1 intron_variant ; MODIFIER silent_mutation Average:46.434; most accessible tissue: Callus, score: 62.407 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005627516 NA 7.28E-06 mr1708 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
vg1005627516 9.68E-06 NA mr1940 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
vg1005627516 NA 5.92E-07 mr1110_2 Ind_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