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Detailed information for vg0620904318:

Variant ID: vg0620904318 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 20904318
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTCTTGTATGCGAAATGATTTATTTATCTTTTTTCTCTTCTCATTAACTTTCTTTGCCACCTTAACTTTTGCTTATGTGACAACGTACTTAACACTTT[G/A]
AAAACTAAGGTGGAGGGTTGGGAGTGCCCTTACTTATCGGTGCTCCTTTTCTTGTCTGTAACCTGGCTGTCCCAATTGATTATATGACCGTGTCTGACGA

Reverse complement sequence

TCGTCAGACACGGTCATATAATCAATTGGGACAGCCAGGTTACAGACAAGAAAAGGAGCACCGATAAGTAAGGGCACTCCCAACCCTCCACCTTAGTTTT[C/T]
AAAGTGTTAAGTACGTTGTCACATAAGCAAAAGTTAAGGTGGCAAAGAAAGTTAATGAGAAGAGAAAAAAGATAAATAAATCATTTCGCATACAAGAAAT

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 85.00% 14.70% 0.30% 0.00% NA
All Indica  2759 99.00% 1.00% 0.00% 0.00% NA
All Japonica  1512 56.30% 42.80% 0.93% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.90% 0.00% 0.00% NA
Temperate Japonica  767 84.90% 13.80% 1.30% 0.00% NA
Tropical Japonica  504 15.90% 83.70% 0.40% 0.00% NA
Japonica Intermediate  241 49.80% 49.40% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg0620904318 G -> A LOC_Os06g35814.1 upstream_gene_variant ; 2602.0bp to feature; MODIFIER silent_mutation Average:57.958; most accessible tissue: Callus, score: 73.741 N N N N
vg0620904318 G -> A LOC_Os06g35830.1 upstream_gene_variant ; 1693.0bp to feature; MODIFIER silent_mutation Average:57.958; most accessible tissue: Callus, score: 73.741 N N N N
vg0620904318 G -> A LOC_Os06g35814-LOC_Os06g35830 intergenic_region ; MODIFIER silent_mutation Average:57.958; most accessible tissue: Callus, score: 73.741 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0620904318 NA 7.98E-07 mr1338 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
vg0620904318 NA 3.37E-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
vg0620904318 NA 3.08E-10 mr1623 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
vg0620904318 NA 2.17E-08 mr1648 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
vg0620904318 NA 2.18E-06 mr1742 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
vg0620904318 NA 4.21E-07 mr1187_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
vg0620904318 NA 2.94E-06 mr1331_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
vg0620904318 NA 1.75E-06 mr1363_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
vg0620904318 NA 1.71E-07 mr1408_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
vg0620904318 NA 1.93E-06 mr1544_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
vg0620904318 NA 1.35E-06 mr1544_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
vg0620904318 3.04E-06 3.43E-10 mr1749_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
vg0620904318 NA 3.45E-11 mr1761_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
vg0620904318 NA 5.24E-07 mr1786_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
vg0620904318 3.39E-07 7.21E-11 mr1821_2 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
vg0620904318 NA 6.70E-06 mr1821_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