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Detailed information for vg1006139083:

Variant ID: vg1006139083 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 6139083
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, A: 0.29, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:


ATACAAATGCGACAAGTTATGTTAGCATGATATGAGGCAACCAAATAAGAAGCATTAAGAATCAATCATGCTCATCCTATACTAAAGCTCGAACAAGAAG[C/A]
AATAAACCAAAATAGTTTTCCAATTGCGATCAACATAGCGGGCCAAAAGCGTATCAATCGCCGGAACATGAAAATTCAAATAAACCAACACTGCAACTTG

Reverse complement sequence

CAAGTTGCAGTGTTGGTTTATTTGAATTTTCATGTTCCGGCGATTGATACGCTTTTGGCCCGCTATGTTGATCGCAATTGGAAAACTATTTTGGTTTATT[G/T]
CTTCTTGTTCGAGCTTTAGTATAGGATGAGCATGATTGATTCTTAATGCTTCTTATTTGGTTGCCTCATATCATGCTAACATAACTTGTCGCATTTGTAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.00% 32.20% 5.48% 7.32% NA
All Indica  2759 75.00% 14.80% 7.21% 2.97% NA
All Japonica  1512 11.40% 68.10% 3.64% 16.93% NA
Aus  269 98.50% 0.00% 0.74% 0.74% NA
Indica I  595 97.30% 0.50% 1.51% 0.67% NA
Indica II  465 72.30% 11.80% 11.61% 4.30% NA
Indica III  913 60.50% 26.90% 8.32% 4.27% NA
Indica Intermediate  786 76.60% 13.40% 7.63% 2.42% NA
Temperate Japonica  767 2.60% 84.60% 1.30% 11.47% NA
Tropical Japonica  504 25.40% 46.40% 4.96% 23.21% NA
Japonica Intermediate  241 10.00% 60.60% 8.30% 21.16% NA
VI/Aromatic  96 55.20% 44.80% 0.00% 0.00% NA
Intermediate  90 45.60% 44.40% 3.33% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1006139083 C -> A LOC_Os10g11090.1 downstream_gene_variant ; 2491.0bp to feature; MODIFIER silent_mutation Average:26.335; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg1006139083 C -> A LOC_Os10g11100.1 intron_variant ; MODIFIER silent_mutation Average:26.335; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg1006139083 C -> DEL N N silent_mutation Average:26.335; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1006139083 NA 2.63E-10 mr1026 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
vg1006139083 NA 9.89E-08 mr1113 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
vg1006139083 NA 4.67E-07 mr1114 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
vg1006139083 NA 5.34E-08 mr1116 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
vg1006139083 NA 1.01E-14 mr1118 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
vg1006139083 5.45E-07 4.16E-17 mr1118 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
vg1006139083 NA 1.25E-09 mr1161 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
vg1006139083 NA 5.46E-08 mr1247 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
vg1006139083 NA 4.50E-26 mr1495 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
vg1006139083 2.61E-08 1.92E-19 mr1495 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
vg1006139083 NA 4.12E-07 mr1496 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
vg1006139083 NA 4.53E-08 mr1794 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
vg1006139083 NA 3.08E-06 mr1936 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
vg1006139083 8.56E-07 8.56E-07 mr1945 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
vg1006139083 NA 2.29E-09 mr1113_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
vg1006139083 NA 5.18E-10 mr1114_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
vg1006139083 NA 2.05E-07 mr1117_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
vg1006139083 NA 4.64E-16 mr1118_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
vg1006139083 8.70E-07 4.45E-17 mr1118_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
vg1006139083 NA 1.85E-07 mr1119_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
vg1006139083 NA 1.74E-10 mr1120_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
vg1006139083 NA 1.27E-09 mr1161_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
vg1006139083 NA 5.55E-06 mr1195_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
vg1006139083 NA 1.43E-10 mr1247_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
vg1006139083 9.04E-08 6.27E-10 mr1258_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
vg1006139083 NA 1.65E-24 mr1495_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
vg1006139083 NA 2.15E-17 mr1495_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
vg1006139083 NA 3.79E-11 mr1794_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