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Detailed information for vg0232485407:

Variant ID: vg0232485407 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 32485407
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCACCAACAACACTCCTTACAAAAATCTCGACTAAACTCGAAACCCTAACTAAACTAGCAACTCAATTACTCTCAAAAGTGATACTGGGAAGACTCACG[C/A]
TCCCCCTCTATTTATTCATGAGGTAGGCAGCCTAAAGCCACGAACCAAACTCATACTAAGAGTCCTAAACACCTTAGGAAACCCTCTAGTACAAGACACA

Reverse complement sequence

TGTGTCTTGTACTAGAGGGTTTCCTAAGGTGTTTAGGACTCTTAGTATGAGTTTGGTTCGTGGCTTTAGGCTGCCTACCTCATGAATAAATAGAGGGGGA[G/T]
CGTGAGTCTTCCCAGTATCACTTTTGAGAGTAATTGAGTTGCTAGTTTAGTTAGGGTTTCGAGTTTAGTCGAGATTTTTGTAAGGAGTGTTGTTGGTGCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.10% 2.90% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 91.10% 8.90% 0.00% 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 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 86.60% 13.40% 0.00% 0.00% NA
Tropical Japonica  504 97.40% 2.60% 0.00% 0.00% NA
Japonica Intermediate  241 92.10% 7.90% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0232485407 C -> A LOC_Os02g53100.1 upstream_gene_variant ; 3610.0bp to feature; MODIFIER silent_mutation Average:25.298; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0232485407 C -> A LOC_Os02g53090.1 intron_variant ; MODIFIER silent_mutation Average:25.298; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0232485407 7.53E-06 7.53E-06 mr1186_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
vg0232485407 5.77E-07 5.77E-07 mr1371_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
vg0232485407 NA 9.32E-06 mr1380_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
vg0232485407 9.45E-06 9.45E-06 mr1494_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
vg0232485407 1.31E-07 1.31E-07 mr1499_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
vg0232485407 8.17E-07 8.17E-07 mr1616_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
vg0232485407 9.50E-06 9.50E-06 mr1876_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
vg0232485407 5.74E-07 1.20E-08 mr1946_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
vg0232485407 5.74E-07 1.20E-08 mr1948_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
vg0232485407 4.47E-07 2.37E-08 mr1977_2 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