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Detailed information for vg0715040944:

Variant ID: vg0715040944 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15040944
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


GGACAAGGAGTGCGTTCATGCCCTGTATGCCTTTGAGTAAGTTTTAATATCCATTAAGAGTATATACATATAATCACGGCTCAACTAACAATTTTGTTTG[C/T]
AGCGACCATTGGATAGTCTTTCTTCTCTATCCAAAGTACAATGAAGTCATCGTCTTAGATTCTCTCGACAAAGACGGCAAGACATATCAGGAATTTCTAA

Reverse complement sequence

TTAGAAATTCCTGATATGTCTTGCCGTCTTTGTCGAGAGAATCTAAGACGATGACTTCATTGTACTTTGGATAGAGAAGAAAGACTATCCAATGGTCGCT[G/A]
CAAACAAAATTGTTAGTTGAGCCGTGATTATATGTATATACTCTTAATGGATATTAAAACTTACTCAAAGGCATACAGGGCATGAACGCACTCCTTGTCC

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 51.40% 46.40% 1.31% 0.83% NA
All Indica  2759 30.00% 67.90% 1.78% 0.33% NA
All Japonica  1512 93.90% 5.90% 0.13% 0.07% NA
Aus  269 26.40% 70.30% 1.86% 1.49% NA
Indica I  595 21.20% 72.60% 5.55% 0.67% NA
Indica II  465 15.70% 84.10% 0.22% 0.00% NA
Indica III  913 33.00% 66.50% 0.22% 0.33% NA
Indica Intermediate  786 41.70% 56.40% 1.65% 0.25% NA
Temperate Japonica  767 88.90% 11.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 1.20% 0.83% 0.41% NA
VI/Aromatic  96 55.20% 14.60% 5.21% 25.00% NA
Intermediate  90 64.40% 33.30% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0715040944 C -> DEL N N silent_mutation Average:37.649; most accessible tissue: Minghui63 flag leaf, score: 61.847 N N N N
vg0715040944 C -> T LOC_Os07g26160.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:37.649; most accessible tissue: Minghui63 flag leaf, score: 61.847 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715040944 NA 3.21E-07 mr1104 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
vg0715040944 NA 1.54E-06 mr1169 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
vg0715040944 NA 1.21E-11 mr1233 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
vg0715040944 NA 6.17E-06 mr1233 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
vg0715040944 7.99E-06 7.99E-06 mr1762 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
vg0715040944 NA 3.19E-07 mr1888 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
vg0715040944 NA 1.69E-07 mr1004_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
vg0715040944 NA 9.59E-07 mr1161_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
vg0715040944 NA 8.58E-07 mr1721_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
vg0715040944 NA 5.78E-06 mr1806_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
vg0715040944 NA 2.31E-06 mr1870_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