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Detailed information for vg0630442371:

Variant ID: vg0630442371 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 30442371
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


CACCTCTCCAAAAGTGCACCGCTGCTATTCGAATGCTAGGATATGGCACACCAGCGGACGCACTAGATGAGGTACTCAAGATTGCAGCGAGCACTTCTTT[G/A]
GAATGTTTGGGAAAATTTGCCGTAGGAATAATTGAATGTTTTGGTAGCGAGTACTTGCGTCCTCCGACAAGTGATGAACTAGAAAAAATTTTACAAGAGA

Reverse complement sequence

TCTCTTGTAAAATTTTTTCTAGTTCATCACTTGTCGGAGGACGCAAGTACTCGCTACCAAAACATTCAATTATTCCTACGGCAAATTTTCCCAAACATTC[C/T]
AAAGAAGTGCTCGCTGCAATCTTGAGTACCTCATCTAGTGCGTCCGCTGGTGTGCCATATCCTAGCATTCGAATAGCAGCGGTGCACTTTTGGAGAGGTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.00% 0.10% 5.67% 47.23% NA
All Indica  2759 33.20% 0.10% 6.78% 59.84% NA
All Japonica  1512 64.20% 0.20% 4.83% 30.75% NA
Aus  269 95.20% 0.00% 0.00% 4.83% NA
Indica I  595 48.40% 0.50% 6.55% 44.54% NA
Indica II  465 13.10% 0.00% 7.53% 79.35% NA
Indica III  913 32.00% 0.00% 6.57% 61.45% NA
Indica Intermediate  786 35.10% 0.10% 6.74% 58.02% NA
Temperate Japonica  767 94.10% 0.10% 0.39% 5.35% NA
Tropical Japonica  504 20.80% 0.20% 12.50% 66.47% NA
Japonica Intermediate  241 59.80% 0.40% 2.90% 36.93% NA
VI/Aromatic  96 38.50% 0.00% 1.04% 60.42% NA
Intermediate  90 42.20% 0.00% 7.78% 50.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0630442371 G -> A LOC_Os06g50290.1 synonymous_variant ; p.Leu615Leu; LOW synonymous_codon Average:9.999; most accessible tissue: Callus, score: 20.768 N N N N
vg0630442371 G -> DEL LOC_Os06g50290.1 N frameshift_variant Average:9.999; most accessible tissue: Callus, score: 20.768 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0630442371 1.85E-06 1.85E-06 mr1590 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
vg0630442371 NA 3.29E-06 mr1657 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
vg0630442371 3.60E-06 3.60E-06 mr1891 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
vg0630442371 NA 9.04E-07 mr1964 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
vg0630442371 3.37E-06 3.37E-06 mr1159_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
vg0630442371 4.69E-06 8.41E-07 mr1312_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
vg0630442371 1.29E-06 1.29E-06 mr1312_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
vg0630442371 8.13E-06 8.14E-06 mr1313_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
vg0630442371 NA 4.14E-06 mr1363_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
vg0630442371 NA 2.20E-06 mr1397_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
vg0630442371 4.15E-06 4.15E-06 mr1453_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
vg0630442371 3.43E-07 2.17E-08 mr1663_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
vg0630442371 2.09E-06 2.09E-06 mr1663_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
vg0630442371 4.67E-06 NA mr1665_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
vg0630442371 1.55E-06 7.02E-07 mr1665_2 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
vg0630442371 9.07E-06 9.07E-06 mr1687_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
vg0630442371 NA 5.48E-06 mr1812_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
vg0630442371 NA 4.17E-06 mr1816_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
vg0630442371 8.81E-06 8.81E-06 mr1832_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
vg0630442371 3.55E-06 3.55E-06 mr1847_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