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Detailed information for vg0702575490:

Variant ID: vg0702575490 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 2575490
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGGCTCCTAATCCATCAAAACCCCCGGACCAAATAAGCCCTAATCCTAATTCCAGTTTTCCCCTTCCTCCCCTCCACGCAGGCCGCCTCTCTCCCCACC[G/A]
GCGCACCTCTTCGTGCCCCTCCCCACCGGCGGTGCCCAACGGATGGCGACGGTAGCAGCCTTCCCCACCGAGCAGCGGCAGTGGTGACGGCAACCTTCTC

Reverse complement sequence

GAGAAGGTTGCCGTCACCACTGCCGCTGCTCGGTGGGGAAGGCTGCTACCGTCGCCATCCGTTGGGCACCGCCGGTGGGGAGGGGCACGAAGAGGTGCGC[C/T]
GGTGGGGAGAGAGGCGGCCTGCGTGGAGGGGAGGAAGGGGAAAACTGGAATTAGGATTAGGGCTTATTTGGTCCGGGGGTTTTGATGGATTAGGAGCCGA

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 98.50% 0.90% 0.59% 0.00% NA
All Indica  2759 99.90% 0.10% 0.07% 0.00% NA
All Japonica  1512 95.70% 2.60% 1.72% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 99.30% 0.40% 0.26% 0.00% NA
Tropical Japonica  504 88.30% 7.10% 4.56% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 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
vg0702575490 G -> A LOC_Os07g05510.1 upstream_gene_variant ; 4849.0bp to feature; MODIFIER silent_mutation Average:72.103; most accessible tissue: Zhenshan97 panicle, score: 85.254 N N N N
vg0702575490 G -> A LOC_Os07g05530.1 upstream_gene_variant ; 4727.0bp to feature; MODIFIER silent_mutation Average:72.103; most accessible tissue: Zhenshan97 panicle, score: 85.254 N N N N
vg0702575490 G -> A LOC_Os07g05520.1 downstream_gene_variant ; 704.0bp to feature; MODIFIER silent_mutation Average:72.103; most accessible tissue: Zhenshan97 panicle, score: 85.254 N N N N
vg0702575490 G -> A LOC_Os07g05510-LOC_Os07g05520 intergenic_region ; MODIFIER silent_mutation Average:72.103; most accessible tissue: Zhenshan97 panicle, score: 85.254 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0702575490 9.02E-06 4.79E-06 mr1070_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
vg0702575490 5.39E-06 NA mr1083_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
vg0702575490 3.18E-07 2.06E-06 mr1085_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
vg0702575490 4.16E-06 1.03E-06 mr1088_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
vg0702575490 1.49E-06 1.49E-06 mr1145_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
vg0702575490 NA 5.53E-08 mr1155_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
vg0702575490 NA 7.43E-07 mr1246_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
vg0702575490 NA 1.05E-07 mr1250_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
vg0702575490 5.25E-06 5.25E-06 mr1264_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
vg0702575490 NA 5.60E-06 mr1404_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
vg0702575490 NA 7.14E-06 mr1437_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
vg0702575490 9.09E-06 5.65E-06 mr1620_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
vg0702575490 NA 4.23E-06 mr1668_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
vg0702575490 NA 2.99E-06 mr1739_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