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Detailed information for vg0334406362:

Variant ID: vg0334406362 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34406362
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCCTTTTGTAATGCAGTTGTGAGATCGGGATCTGTCCGCAGCCCAACATGACTGTACATCTACTCTATAATAAAGAGACCTCTGTTGCTGTGATAATCT[G/A]
TCTTCCTGTGATATCAGCACTGTGTCCTGGGACTGGTATCGATTAACAGGTTAAATTGGAGCGTCACGGGCTAGTTCCGGTCGGTACTAGTTCGGGGCGT

Reverse complement sequence

ACGCCCCGAACTAGTACCGACCGGAACTAGCCCGTGACGCTCCAATTTAACCTGTTAATCGATACCAGTCCCAGGACACAGTGCTGATATCACAGGAAGA[C/T]
AGATTATCACAGCAACAGAGGTCTCTTTATTATAGAGTAGATGTACAGTCATGTTGGGCTGCGGACAGATCCCGATCTCACAACTGCATTACAAAAGGGA

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 40.50% 1.50% 8.89% 49.13% NA
All Indica  2759 14.90% 0.00% 11.09% 74.01% NA
All Japonica  1512 90.10% 4.50% 4.10% 1.32% NA
Aus  269 2.20% 0.00% 16.36% 81.41% NA
Indica I  595 13.80% 0.00% 6.22% 80.00% NA
Indica II  465 10.10% 0.00% 6.24% 83.66% NA
Indica III  913 18.60% 0.00% 17.96% 63.42% NA
Indica Intermediate  786 14.20% 0.00% 9.67% 76.08% NA
Temperate Japonica  767 86.40% 7.30% 6.13% 0.13% NA
Tropical Japonica  504 94.00% 0.60% 1.79% 3.57% NA
Japonica Intermediate  241 93.40% 3.70% 2.49% 0.41% NA
VI/Aromatic  96 91.70% 0.00% 3.12% 5.21% NA
Intermediate  90 53.30% 1.10% 5.56% 40.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0334406362 G -> A LOC_Os03g60524.1 upstream_gene_variant ; 743.0bp to feature; MODIFIER silent_mutation Average:66.919; most accessible tissue: Zhenshan97 flower, score: 89.027 N N N N
vg0334406362 G -> A LOC_Os03g60530.1 upstream_gene_variant ; 731.0bp to feature; MODIFIER silent_mutation Average:66.919; most accessible tissue: Zhenshan97 flower, score: 89.027 N N N N
vg0334406362 G -> A LOC_Os03g60530.3 upstream_gene_variant ; 731.0bp to feature; MODIFIER silent_mutation Average:66.919; most accessible tissue: Zhenshan97 flower, score: 89.027 N N N N
vg0334406362 G -> A LOC_Os03g60540.1 downstream_gene_variant ; 4500.0bp to feature; MODIFIER silent_mutation Average:66.919; most accessible tissue: Zhenshan97 flower, score: 89.027 N N N N
vg0334406362 G -> A LOC_Os03g60524-LOC_Os03g60530 intergenic_region ; MODIFIER silent_mutation Average:66.919; most accessible tissue: Zhenshan97 flower, score: 89.027 N N N N
vg0334406362 G -> DEL N N silent_mutation Average:66.919; most accessible tissue: Zhenshan97 flower, score: 89.027 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334406362 3.00E-06 NA mr1627 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