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Detailed information for vg1012224194:

Variant ID: vg1012224194 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 12224194
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGGTATACCTACATATCCATGATCCTGGGTCTCGCAATGCACGGCCGCGGCGAGGATGCCCTGTCTCTATTCGCCAGCATGCAACGAGCCGGCGTGAC[G/A]
CCGAACGAGGTGACCCTCCTCGGCGTCCTCACGGCGTGCTGTCATGCCGGACTCATCGAGGAGGGGCTCCAGCAACTCGACGCCATGAGGAGGAACGAGA

Reverse complement sequence

TCTCGTTCCTCCTCATGGCGTCGAGTTGCTGGAGCCCCTCCTCGATGAGTCCGGCATGACAGCACGCCGTGAGGACGCCGAGGAGGGTCACCTCGTTCGG[C/T]
GTCACGCCGGCTCGTTGCATGCTGGCGAATAGAGACAGGGCATCCTCGCCGCGGCCGTGCATTGCGAGACCCAGGATCATGGATATGTAGGTATACCGGC

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 31.10% 17.70% 1.31% 49.89% NA
All Indica  2759 2.50% 28.50% 1.92% 67.05% NA
All Japonica  1512 89.30% 0.40% 0.20% 10.12% NA
Aus  269 1.90% 9.30% 1.86% 86.99% NA
Indica I  595 3.90% 7.10% 3.03% 86.05% NA
Indica II  465 2.80% 36.10% 1.72% 59.35% NA
Indica III  913 1.40% 33.60% 1.10% 63.86% NA
Indica Intermediate  786 2.50% 34.40% 2.16% 60.94% NA
Temperate Japonica  767 97.00% 0.30% 0.13% 2.61% NA
Tropical Japonica  504 81.50% 0.40% 0.40% 17.66% NA
Japonica Intermediate  241 80.90% 0.80% 0.00% 18.26% NA
VI/Aromatic  96 6.20% 3.10% 1.04% 89.58% NA
Intermediate  90 43.30% 17.80% 0.00% 38.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1012224194 G -> A LOC_Os10g23830.1 synonymous_variant ; p.Thr96Thr; LOW synonymous_codon Average:14.255; most accessible tissue: Callus, score: 56.934 N N N N
vg1012224194 G -> DEL LOC_Os10g23830.1 N frameshift_variant Average:14.255; most accessible tissue: Callus, score: 56.934 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1012224194 NA 1.01E-07 mr1157 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
vg1012224194 NA 1.58E-06 mr1157 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
vg1012224194 NA 1.60E-09 mr1328 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
vg1012224194 7.00E-06 2.25E-08 mr1328 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
vg1012224194 NA 2.84E-10 mr1446 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
vg1012224194 3.23E-06 2.25E-08 mr1446 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
vg1012224194 NA 8.08E-06 mr1236_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
vg1012224194 NA 9.86E-06 mr1419_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
vg1012224194 3.07E-07 9.38E-14 mr1446_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
vg1012224194 1.84E-06 8.21E-10 mr1446_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
vg1012224194 NA 3.75E-06 mr1567_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