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Detailed information for vg0107540423:

Variant ID: vg0107540423 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 7540423
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAAGTCACATTACCTTAATTATTTCTAGTCTTTTAATGATAGATATATAGTTCAAATTGTCTTTTCTTTCTTCTCTCTTAAAAACATGCAATCTCAATTA[C/T]
TTTTAGCTCAAAATTATATCAAATTGTTTTAATTTTGTACGTATTATGTAACTTAATTTTCTACAGCAACGCGACCAGATGTTCATATAGTATCTTATAA

Reverse complement sequence

TTATAAGATACTATATGAACATCTGGTCGCGTTGCTGTAGAAAATTAAGTTACATAATACGTACAAAATTAAAACAATTTGATATAATTTTGAGCTAAAA[G/A]
TAATTGAGATTGCATGTTTTTAAGAGAGAAGAAAGAAAAGACAATTTGAACTATATATCTATCATTAAAAGACTAGAAATAATTAAGGTAATGTGACTTA

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 93.10% 6.80% 0.11% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 79.20% 20.50% 0.33% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 98.30% 1.60% 0.13% 0.00% NA
Tropical Japonica  504 46.60% 52.60% 0.79% 0.00% NA
Japonica Intermediate  241 86.30% 13.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0107540423 C -> T LOC_Os01g13510.1 upstream_gene_variant ; 3248.0bp to feature; MODIFIER silent_mutation Average:33.976; most accessible tissue: Zhenshan97 flower, score: 43.307 N N N N
vg0107540423 C -> T LOC_Os01g13500-LOC_Os01g13510 intergenic_region ; MODIFIER silent_mutation Average:33.976; most accessible tissue: Zhenshan97 flower, score: 43.307 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0107540423 NA 5.64E-06 mr1213 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
vg0107540423 NA 5.46E-07 mr1403 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
vg0107540423 NA 1.59E-14 mr1410 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
vg0107540423 NA 9.94E-08 mr1668 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
vg0107540423 NA 6.39E-07 mr1693 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
vg0107540423 NA 1.56E-06 mr1741 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
vg0107540423 NA 5.68E-15 mr1410_2 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
vg0107540423 NA 5.00E-07 mr1668_2 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