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Detailed information for vg0702624412:

Variant ID: vg0702624412 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 2624412
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATCTGCAGTACGTGGCATGCATTACATATATTTAAATATGTTAATTAATTCGATCTGGATTAATCAAAATTAACATATCTCTATCTCTACTACTTAAAA[C/A]
ATAAGAGGTGCTTCCATTGTCCGTCAAAAAAATCGGGCGAAAAAAACCAAATTTATCCGATCTAAAAAACTGAGCGAAAGAAAACGTCCAGAAAAAAGAG

Reverse complement sequence

CTCTTTTTTCTGGACGTTTTCTTTCGCTCAGTTTTTTAGATCGGATAAATTTGGTTTTTTTCGCCCGATTTTTTTGACGGACAATGGAAGCACCTCTTAT[G/T]
TTTTAAGTAGTAGAGATAGAGATATGTTAATTTTGATTAATCCAGATCGAATTAATTAACATATTTAAATATATGTAATGCATGCCACGTACTGCAGATT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.60% 10.30% 3.09% 0.00% NA
All Indica  2759 98.60% 0.80% 0.54% 0.00% NA
All Japonica  1512 61.40% 30.30% 8.33% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.80% 2.70% 1.51% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 0.50% 0.76% 0.00% NA
Temperate Japonica  767 39.60% 47.20% 13.17% 0.00% NA
Tropical Japonica  504 94.20% 3.20% 2.58% 0.00% NA
Japonica Intermediate  241 61.80% 33.20% 4.98% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 6.70% 5.56% 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
vg0702624412 C -> A LOC_Os07g05600.1 upstream_gene_variant ; 3941.0bp to feature; MODIFIER silent_mutation Average:29.358; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0702624412 C -> A LOC_Os07g05590.1 intron_variant ; MODIFIER silent_mutation Average:29.358; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0702624412 NA 1.44E-06 mr1206 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
vg0702624412 NA 8.92E-07 mr1229 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
vg0702624412 1.71E-06 2.39E-07 mr1596 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
vg0702624412 6.43E-06 7.02E-08 mr1596 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
vg0702624412 NA 1.24E-07 mr1763 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
vg0702624412 NA 5.92E-06 mr1763 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
vg0702624412 NA 9.81E-06 mr1775 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
vg0702624412 4.46E-06 NA mr1789 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
vg0702624412 NA 3.23E-07 mr1880 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
vg0702624412 NA 7.63E-08 mr1137_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
vg0702624412 NA 8.08E-06 mr1617_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
vg0702624412 NA 1.46E-08 mr1880_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
vg0702624412 NA 4.23E-07 mr1880_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