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Detailed information for vg0412432479:

Variant ID: vg0412432479 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 12432479
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCCATAAAGATATGCTGTCACTACGTCCATCTACTGTATAAATAGACGATTTTGTACTGCCAATGATATTAAATATCGGAAAGTTATACCACTCATAACT[G/A]
GAGAGTAAGTTTCATTGAAATCAACGCCAGGTTTTTGCGTAAAACCTTGTGCTACAAGCCTTGCTTTATATCTCACCACCTCGTTGTTTTCGTTCCGTTT

Reverse complement sequence

AAACGGAACGAAAACAACGAGGTGGTGAGATATAAAGCAAGGCTTGTAGCACAAGGTTTTACGCAAAAACCTGGCGTTGATTTCAATGAAACTTACTCTC[C/T]
AGTTATGAGTGGTATAACTTTCCGATATTTAATATCATTGGCAGTACAAAATCGTCTATTTATACAGTAGATGGACGTAGTGACAGCATATCTTTATGGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.20% 9.60% 25.20% 18.03% NA
All Indica  2759 36.00% 0.60% 38.35% 25.08% NA
All Japonica  1512 65.30% 27.90% 3.90% 2.91% NA
Aus  269 44.60% 0.00% 20.07% 35.32% NA
Indica I  595 25.20% 0.50% 34.12% 40.17% NA
Indica II  465 20.90% 1.30% 52.04% 25.81% NA
Indica III  913 52.10% 0.30% 32.86% 14.68% NA
Indica Intermediate  786 34.20% 0.60% 39.82% 25.32% NA
Temperate Japonica  767 97.10% 1.20% 1.17% 0.52% NA
Tropical Japonica  504 15.10% 69.80% 8.13% 6.94% NA
Japonica Intermediate  241 68.90% 25.30% 3.73% 2.07% NA
VI/Aromatic  96 90.60% 2.10% 2.08% 5.21% NA
Intermediate  90 47.80% 14.40% 20.00% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0412432479 G -> DEL N N silent_mutation Average:7.752; most accessible tissue: Callus, score: 13.324 N N N N
vg0412432479 G -> A LOC_Os04g21970.1 downstream_gene_variant ; 2472.0bp to feature; MODIFIER silent_mutation Average:7.752; most accessible tissue: Callus, score: 13.324 N N N N
vg0412432479 G -> A LOC_Os04g21960.1 intron_variant ; MODIFIER silent_mutation Average:7.752; most accessible tissue: Callus, score: 13.324 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0412432479 NA 3.26E-24 mr1301 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
vg0412432479 NA 7.17E-14 mr1301 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
vg0412432479 NA 4.42E-06 mr1364 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
vg0412432479 NA 8.14E-07 mr1401 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
vg0412432479 NA 3.21E-06 mr1443 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
vg0412432479 NA 6.94E-08 mr1552 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
vg0412432479 NA 2.64E-07 mr1554 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
vg0412432479 1.15E-06 8.35E-06 mr1807 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
vg0412432479 NA 2.52E-10 mr1905 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
vg0412432479 NA 4.66E-08 mr1993 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
vg0412432479 NA 5.14E-10 mr1993 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
vg0412432479 NA 8.06E-13 mr1178_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
vg0412432479 NA 3.05E-20 mr1301_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
vg0412432479 NA 3.80E-06 mr1398_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
vg0412432479 NA 1.95E-06 mr1449_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
vg0412432479 NA 1.07E-15 mr1539_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
vg0412432479 NA 1.24E-17 mr1540_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
vg0412432479 NA 1.14E-08 mr1696_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
vg0412432479 NA 1.21E-15 mr1732_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
vg0412432479 NA 3.88E-09 mr1905_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
vg0412432479 NA 3.24E-09 mr1942_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
vg0412432479 NA 4.20E-10 mr1993_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
vg0412432479 NA 2.31E-11 mr1993_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