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Detailed information for vg0613389030:

Variant ID: vg0613389030 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13389030
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.02, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


ATACTCTACTTCTAATATTCCTTATTTTTAATTCCAAGTTTATATTATTTCCTAATTGTATTTCTATATGGACTCTATACTCTACTTCTAATATTCCTTA[C/T]
TTTTAATTCCGAATTTCAGTTATTTCCTAATTATATTTCTATATGGACTCTATACTCTACTTCTAATATTCCTTATTTTTAATTCCGAATTTCAGTTATT

Reverse complement sequence

AATAACTGAAATTCGGAATTAAAAATAAGGAATATTAGAAGTAGAGTATAGAGTCCATATAGAAATATAATTAGGAAATAACTGAAATTCGGAATTAAAA[G/A]
TAAGGAATATTAGAAGTAGAGTATAGAGTCCATATAGAAATACAATTAGGAAATAATATAAACTTGGAATTAAAAATAAGGAATATTAGAAGTAGAGTAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 32.40% 1.10% 10.88% 55.67% NA
All Indica  2759 4.20% 1.10% 7.18% 87.53% NA
All Japonica  1512 90.60% 0.30% 6.48% 2.58% NA
Aus  269 1.50% 5.20% 44.61% 48.70% NA
Indica I  595 5.40% 1.20% 11.43% 82.02% NA
Indica II  465 4.90% 0.20% 2.15% 92.69% NA
Indica III  913 1.90% 1.00% 5.04% 92.11% NA
Indica Intermediate  786 5.50% 1.80% 9.41% 83.33% NA
Temperate Japonica  767 96.50% 0.10% 0.13% 3.26% NA
Tropical Japonica  504 81.00% 0.80% 16.47% 1.79% NA
Japonica Intermediate  241 92.10% 0.00% 5.81% 2.07% NA
VI/Aromatic  96 2.10% 0.00% 85.42% 12.50% NA
Intermediate  90 44.40% 0.00% 17.78% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0613389030 C -> T LOC_Os06g22940.1 downstream_gene_variant ; 2483.0bp to feature; MODIFIER silent_mutation Average:9.648; most accessible tissue: Zhenshan97 root, score: 18.731 N N N N
vg0613389030 C -> T LOC_Os06g22919.1 intron_variant ; MODIFIER silent_mutation Average:9.648; most accessible tissue: Zhenshan97 root, score: 18.731 N N N N
vg0613389030 C -> T LOC_Os06g22919.3 intron_variant ; MODIFIER silent_mutation Average:9.648; most accessible tissue: Zhenshan97 root, score: 18.731 N N N N
vg0613389030 C -> T LOC_Os06g22919.4 intron_variant ; MODIFIER silent_mutation Average:9.648; most accessible tissue: Zhenshan97 root, score: 18.731 N N N N
vg0613389030 C -> T LOC_Os06g22919.2 intron_variant ; MODIFIER silent_mutation Average:9.648; most accessible tissue: Zhenshan97 root, score: 18.731 N N N N
vg0613389030 C -> DEL N N silent_mutation Average:9.648; most accessible tissue: Zhenshan97 root, score: 18.731 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613389030 3.02E-14 5.15E-83 mr1033 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
vg0613389030 2.18E-07 6.08E-13 mr1033 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
vg0613389030 2.74E-11 3.17E-16 mr1033 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
vg0613389030 NA 3.86E-07 mr1064 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
vg0613389030 NA 4.22E-07 mr1076 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
vg0613389030 NA 3.36E-07 mr1082 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
vg0613389030 NA 2.26E-06 mr1145 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
vg0613389030 1.47E-11 3.31E-47 mr1176 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
vg0613389030 2.56E-06 7.67E-11 mr1176 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
vg0613389030 8.60E-08 1.32E-10 mr1176 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
vg0613389030 NA 9.26E-11 mr1301 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
vg0613389030 NA 2.30E-10 mr1410 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
vg0613389030 NA 1.26E-06 mr1436 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
vg0613389030 NA 7.19E-06 mr1437 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
vg0613389030 3.52E-08 3.52E-08 mr1536 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
vg0613389030 NA 3.52E-08 mr1560 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
vg0613389030 1.47E-15 1.80E-110 mr1033_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
vg0613389030 NA 1.38E-16 mr1033_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
vg0613389030 1.67E-13 1.35E-21 mr1033_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
vg0613389030 NA 8.31E-19 mr1165_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
vg0613389030 NA 2.71E-20 mr1276_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
vg0613389030 6.66E-07 NA mr1536_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
vg0613389030 4.78E-09 1.09E-10 mr1536_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
vg0613389030 NA 9.30E-08 mr1548_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
vg0613389030 NA 7.25E-08 mr1993_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