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Detailed information for vg0607378850:

Variant ID: vg0607378850 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 7378850
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATTGGCCGTAGAACACCGGTCGCATTATTTTATTATTTCCAGGGATAAAAGAGGTGAGATAGTTTTCTAAATACCCGGATTGCCCCTTCTCTTTCCTTC[T/A]
TTTTCTCCTTCTCCTTTCTTCTTTTCCCCCTTCCCGTTGACATCGTCGGGAACGGCATGACGGCCTCAGAGAGCAGTGGGGCGAGGTCAGCACGACGTGG

Reverse complement sequence

CCACGTCGTGCTGACCTCGCCCCACTGCTCTCTGAGGCCGTCATGCCGTTCCCGACGATGTCAACGGGAAGGGGGAAAAGAAGAAAGGAGAAGGAGAAAA[A/T]
GAAGGAAAGAGAAGGGGCAATCCGGGTATTTAGAAAACTATCTCACCTCTTTTATCCCTGGAAATAATAAAATAATGCGACCGGTGTTCTACGGCCAATT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 39.50% 1.60% 1.06% 57.79% NA
All Indica  2759 4.40% 0.10% 0.76% 94.74% NA
All Japonica  1512 98.40% 0.30% 0.07% 1.26% NA
Aus  269 68.00% 0.40% 10.04% 21.56% NA
Indica I  595 2.50% 0.00% 0.67% 96.81% NA
Indica II  465 4.30% 0.00% 0.43% 95.27% NA
Indica III  913 3.20% 0.10% 0.55% 96.17% NA
Indica Intermediate  786 7.40% 0.10% 1.27% 91.22% NA
Temperate Japonica  767 98.80% 0.00% 0.13% 1.04% NA
Tropical Japonica  504 99.00% 0.00% 0.00% 0.99% NA
Japonica Intermediate  241 95.90% 1.70% 0.00% 2.49% NA
VI/Aromatic  96 26.00% 68.80% 0.00% 5.21% NA
Intermediate  90 56.70% 3.30% 1.11% 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
vg0607378850 T -> A LOC_Os06g13420.1 stop_gained ; p.Arg242*; HIGH stop_gained Average:26.613; most accessible tissue: Callus, score: 44.026 N N N N
vg0607378850 T -> DEL LOC_Os06g13420.1 N frameshift_variant Average:26.613; most accessible tissue: Callus, score: 44.026 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0607378850 2.73E-07 NA mr1707 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
vg0607378850 2.22E-06 2.07E-06 mr1707 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
vg0607378850 NA 1.96E-06 mr1973 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
vg0607378850 NA 1.91E-13 mr1138_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
vg0607378850 8.40E-07 NA mr1728_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
vg0607378850 NA 2.54E-06 mr1728_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
vg0607378850 3.69E-06 NA mr1860_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
vg0607378850 NA 4.22E-07 mr1860_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
vg0607378850 3.29E-06 NA mr1970_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
vg0607378850 9.81E-09 NA mr1973_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
vg0607378850 2.35E-06 1.41E-10 mr1973_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