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Detailed information for vg0619153237:

Variant ID: vg0619153237 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19153237
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


GCAATGTTTTTCGTGATTAGTCTCACATTACACATTGATGATAATTGTGATAAATAATTTGACTCCTGGTTTGGAATGGTATATTCCTGGTATGGAGGTT[A/T]
GATTTGTACAACCGGGGTTGGTTGTTCAAATAAGGTTGGGCCTATGTAACACGGGTGTGTTGTATGGTGTTTATCTAATACTGTTTAATTATTCAACTGT

Reverse complement sequence

ACAGTTGAATAATTAAACAGTATTAGATAAACACCATACAACACACCCGTGTTACATAGGCCCAACCTTATTTGAACAACCAACCCCGGTTGTACAAATC[T/A]
AACCTCCATACCAGGAATATACCATTCCAAACCAGGAGTCAAATTATTTATCACAATTATCATCAATGTGTAATGTGAGACTAATCACGAAAAACATTGC

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 66.30% 31.10% 2.41% 0.21% NA
All Indica  2759 94.30% 2.80% 2.90% 0.00% NA
All Japonica  1512 7.60% 89.70% 1.98% 0.66% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 93.80% 1.70% 4.54% 0.00% NA
Indica II  465 95.10% 3.90% 1.08% 0.00% NA
Indica III  913 97.80% 0.90% 1.31% 0.00% NA
Indica Intermediate  786 90.10% 5.30% 4.58% 0.00% NA
Temperate Japonica  767 5.00% 92.30% 1.43% 1.30% NA
Tropical Japonica  504 12.10% 86.70% 1.19% 0.00% NA
Japonica Intermediate  241 6.60% 88.00% 5.39% 0.00% NA
VI/Aromatic  96 94.80% 4.20% 1.04% 0.00% NA
Intermediate  90 64.40% 32.20% 3.33% 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
vg0619153237 A -> T LOC_Os06g32900.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:49.351; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N
vg0619153237 A -> T LOC_Os06g32910.1 downstream_gene_variant ; 4001.0bp to feature; MODIFIER silent_mutation Average:49.351; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N
vg0619153237 A -> DEL N N silent_mutation Average:49.351; 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
vg0619153237 2.37E-06 NA mr1071 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
vg0619153237 4.23E-06 NA mr1140 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
vg0619153237 NA 9.20E-10 mr1354 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
vg0619153237 9.63E-06 NA mr1395 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
vg0619153237 NA 4.22E-06 mr1408 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
vg0619153237 8.15E-06 NA mr1618 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
vg0619153237 NA 4.40E-21 mr1676 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
vg0619153237 NA 3.71E-16 mr1900 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
vg0619153237 NA 1.18E-06 mr1900 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
vg0619153237 NA 3.07E-21 mr1042_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
vg0619153237 NA 3.50E-10 mr1354_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
vg0619153237 NA 2.05E-06 mr1479_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
vg0619153237 NA 2.26E-11 mr1667_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
vg0619153237 NA 5.38E-08 mr1681_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