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Detailed information for vg0709674359:

Variant ID: vg0709674359 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 9674359
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTGGGGTTATATATTGCGGATGAGAGGTGGGCCGCTTATGATGACAGCTCAGTATGGGTATTCCTCGACGCCGGTATATAATCCTAAGTTAATTCCCT[G/A]
GGGAGGGTATTCCTCCGTATTTAGCCCCGGTTGTATGGTCATGATGGGCTGTCATAAGGAATTCGGCAGTCAGGGGTGGCTTCTCGAAGTACCAGGAGGG

Reverse complement sequence

CCCTCCTGGTACTTCGAGAAGCCACCCCTGACTGCCGAATTCCTTATGACAGCCCATCATGACCATACAACCGGGGCTAAATACGGAGGAATACCCTCCC[C/T]
AGGGAATTAACTTAGGATTATATACCGGCGTCGAGGAATACCCATACTGAGCTGTCATCATAAGCGGCCCACCTCTCATCCGCAATATATAACCCCAAAT

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 91.00% 4.70% 2.07% 2.14% NA
All Indica  2759 96.50% 0.20% 1.78% 1.52% NA
All Japonica  1512 82.20% 11.40% 2.58% 3.84% NA
Aus  269 94.10% 4.50% 1.49% 0.00% NA
Indica I  595 94.50% 0.00% 2.69% 2.86% NA
Indica II  465 97.00% 0.40% 1.51% 1.08% NA
Indica III  913 98.50% 0.00% 0.99% 0.55% NA
Indica Intermediate  786 95.50% 0.40% 2.16% 1.91% NA
Temperate Japonica  767 82.90% 9.80% 1.30% 6.00% NA
Tropical Japonica  504 88.70% 4.80% 4.37% 2.18% NA
Japonica Intermediate  241 66.40% 30.30% 2.90% 0.41% NA
VI/Aromatic  96 65.60% 29.20% 4.17% 1.04% NA
Intermediate  90 90.00% 7.80% 2.22% 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
vg0709674359 G -> DEL N N silent_mutation Average:47.954; most accessible tissue: Minghui63 young leaf, score: 65.92 N N N N
vg0709674359 G -> A LOC_Os07g16510.1 downstream_gene_variant ; 1766.0bp to feature; MODIFIER silent_mutation Average:47.954; most accessible tissue: Minghui63 young leaf, score: 65.92 N N N N
vg0709674359 G -> A LOC_Os07g16500.1 intron_variant ; MODIFIER silent_mutation Average:47.954; most accessible tissue: Minghui63 young leaf, score: 65.92 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0709674359 6.70E-07 NA mr1117 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
vg0709674359 2.48E-06 NA mr1119 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
vg0709674359 4.24E-06 NA mr1119 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
vg0709674359 5.31E-06 NA mr1242 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
vg0709674359 5.86E-07 NA mr1496 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
vg0709674359 3.60E-06 NA mr1496 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
vg0709674359 NA 3.51E-06 mr1652 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
vg0709674359 NA 7.39E-06 mr1788 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
vg0709674359 NA 5.80E-07 mr1807 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
vg0709674359 7.86E-06 NA mr1113_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
vg0709674359 8.12E-07 NA mr1114_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
vg0709674359 3.41E-08 NA mr1117_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
vg0709674359 4.18E-06 NA mr1117_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
vg0709674359 4.20E-07 NA mr1118_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
vg0709674359 8.23E-07 NA mr1118_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
vg0709674359 9.30E-07 NA mr1119_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
vg0709674359 1.33E-06 NA mr1120_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
vg0709674359 6.30E-06 NA mr1240_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
vg0709674359 9.87E-06 NA mr1240_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
vg0709674359 4.38E-06 NA mr1242_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
vg0709674359 NA 6.14E-06 mr1458_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
vg0709674359 6.69E-08 NA mr1496_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
vg0709674359 7.82E-07 NA mr1496_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
vg0709674359 9.74E-08 NA mr1563_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
vg0709674359 NA 2.48E-06 mr1788_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