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Detailed information for vg0706127235:

Variant ID: vg0706127235 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 6127235
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGAACCAAGTATTTCCCATCTGCGTAATCCCACCACCACAGCGTACTTCTATGGGACCCAACCGGAAGTTGGGGATATACGTTGGTTATGAGACTTTGT[C/T]
CATAATCAAGTATCTTGAGTCTATGACTATGGATCTTCATACGGCTCGGTACGCTGATTGTATCTTTGATGAGGACTATTTTCCCAGCATTTGGGGGAGA

Reverse complement sequence

TCTCCCCCAAATGCTGGGAAAATAGTCCTCATCAAAGATACAATCAGCGTACCGAGCCGTATGAAGATCCATAGTCATAGACTCAAGATACTTGATTATG[G/A]
ACAAAGTCTCATAACCAACGTATATCCCCAACTTCCGGTTGGGTCCCATAGAAGTACGCTGTGGTGGTGGGATTACGCAGATGGGAAATACTTGGTTCTT

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 93.40% 2.70% 3.89% 0.00% NA
All Indica  2759 90.70% 4.20% 5.11% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 81.00% 5.20% 13.75% 0.00% NA
Indica I  595 84.70% 5.70% 9.58% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 91.30% 4.50% 4.16% 0.00% NA
Indica Intermediate  786 89.10% 5.10% 5.85% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 0.00% 6.67% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0706127235 C -> T LOC_Os07g11090.1 upstream_gene_variant ; 1032.0bp to feature; MODIFIER silent_mutation Average:50.538; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N
vg0706127235 C -> T LOC_Os07g11080.1 intron_variant ; MODIFIER silent_mutation Average:50.538; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0706127235 NA 2.89E-07 mr1213 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
vg0706127235 NA 9.84E-06 mr1246 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
vg0706127235 NA 3.94E-07 mr1063_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
vg0706127235 4.92E-06 6.89E-06 mr1348_2 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
vg0706127235 NA 5.05E-06 mr1469_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
vg0706127235 NA 1.62E-06 mr1511_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
vg0706127235 NA 6.87E-06 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
vg0706127235 NA 1.58E-06 mr1743_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