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Detailed information for vg0700359527:

Variant ID: vg0700359527 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 359527
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACACGGAAACCCATAACCACACTTAAAATGGGACGAAGGGAGTAGTTTGACAGATACATCAAATTCTGCAGATAAGTTGAGAACAAGGCTAGTTTCACTT[T/G]
AACTGCAGACTGCCAAGTTGATATTAATATTATACTGTGCCACACCTGATCTAATTAAGTTTCCCATTGTTCTCGAGGTCCTGCTGATCATCATCATCCA

Reverse complement sequence

TGGATGATGATGATCAGCAGGACCTCGAGAACAATGGGAAACTTAATTAGATCAGGTGTGGCACAGTATAATATTAATATCAACTTGGCAGTCTGCAGTT[A/C]
AAGTGAAACTAGCCTTGTTCTCAACTTATCTGCAGAATTTGATGTATCTGTCAAACTACTCCCTTCGTCCCATTTTAAGTGTGGTTATGGGTTTCCGTGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.90% 21.00% 3.15% 0.00% NA
All Indica  2759 95.90% 3.30% 0.80% 0.00% NA
All Japonica  1512 51.30% 41.00% 7.74% 0.00% NA
Aus  269 6.30% 93.70% 0.00% 0.00% NA
Indica I  595 99.30% 0.30% 0.34% 0.00% NA
Indica II  465 94.20% 2.20% 3.66% 0.00% NA
Indica III  913 95.90% 4.10% 0.00% 0.00% NA
Indica Intermediate  786 94.40% 5.20% 0.38% 0.00% NA
Temperate Japonica  767 17.30% 73.00% 9.65% 0.00% NA
Tropical Japonica  504 92.70% 3.40% 3.97% 0.00% NA
Japonica Intermediate  241 72.60% 17.80% 9.54% 0.00% NA
VI/Aromatic  96 89.60% 6.20% 4.17% 0.00% NA
Intermediate  90 67.80% 25.60% 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
vg0700359527 T -> G LOC_Os07g01570.1 upstream_gene_variant ; 606.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0700359527 T -> G LOC_Os07g01580.1 downstream_gene_variant ; 4785.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0700359527 T -> G LOC_Os07g01570-LOC_Os07g01580 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0700359527 4.27E-06 4.56E-22 mr1300 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
vg0700359527 NA 8.41E-07 mr1300 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
vg0700359527 3.38E-11 2.14E-40 mr1310 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
vg0700359527 2.11E-07 5.30E-12 mr1310 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
vg0700359527 3.55E-11 9.93E-44 mr1926 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
vg0700359527 2.29E-06 1.79E-11 mr1926 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
vg0700359527 3.28E-07 1.53E-13 mr1959 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
vg0700359527 1.55E-06 2.18E-08 mr1959 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
vg0700359527 NA 4.15E-06 mr1977 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
vg0700359527 1.93E-08 8.89E-36 mr1310_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
vg0700359527 NA 2.70E-11 mr1310_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
vg0700359527 2.23E-06 NA mr1902_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
vg0700359527 2.68E-06 1.18E-17 mr1959_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
vg0700359527 NA 2.12E-09 mr1959_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