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Detailed information for vg1005044043:

Variant ID: vg1005044043 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5044043
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


TGTACTAGACAGCTTCACATATTTATGATACTAATATATTGATTAACTTCAATGCATGCAGTTGCCAAGATTAGAACGTCGAACAAGCTTTGACGATACA[G/A]
ACATCACAAATGTCCAGCGTGATCTGTGCCATTTCATCCACCATGAGTGCTGTCATGTGAAAGGAGATTTCTTCGACCCAGAGGGTGCCCTAGCGACAAG

Reverse complement sequence

CTTGTCGCTAGGGCACCCTCTGGGTCGAAGAAATCTCCTTTCACATGACAGCACTCATGGTGGATGAAATGGCACAGATCACGCTGGACATTTGTGATGT[C/T]
TGTATCGTCAAAGCTTGTTCGACGTTCTAATCTTGGCAACTGCATGCATTGAAGTTAATCAATATATTAGTATCATAAATATGTGAAGCTGTCTAGTACA

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 64.10% 2.90% 0.66% 32.40% NA
All Indica  2759 56.60% 4.90% 0.80% 37.73% NA
All Japonica  1512 71.40% 0.00% 0.53% 28.04% NA
Aus  269 85.10% 0.00% 0.37% 14.50% NA
Indica I  595 49.90% 16.10% 1.51% 32.44% NA
Indica II  465 51.00% 2.80% 0.65% 45.59% NA
Indica III  913 62.50% 0.20% 0.66% 36.58% NA
Indica Intermediate  786 58.10% 2.90% 0.51% 38.42% NA
Temperate Japonica  767 80.80% 0.00% 0.13% 19.04% NA
Tropical Japonica  504 59.30% 0.00% 0.79% 39.88% NA
Japonica Intermediate  241 66.80% 0.00% 1.24% 31.95% NA
VI/Aromatic  96 91.70% 0.00% 0.00% 8.33% NA
Intermediate  90 77.80% 1.10% 0.00% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1005044043 G -> A LOC_Os10g09330.1 missense_variant ; p.Asp32Asn; MODERATE nonsynonymous_codon ; D32N Average:15.426; most accessible tissue: Callus, score: 49.421 benign 1.269 DELETERIOUS 0.03
vg1005044043 G -> DEL LOC_Os10g09330.1 N frameshift_variant Average:15.426; most accessible tissue: Callus, score: 49.421 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005044043 8.47E-07 8.38E-08 mr1519_2 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