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Detailed information for vg0621183896:

Variant ID: vg0621183896 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21183896
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGGTAAATAAAATGCTACCTACTCACCGGTAAATTTTTTGAATAAGACGAGTGGTCAAACAGTACAAGCAAAAACTCAAAATCCCTTATATTATGGAAC[A/G]
GAGGGAGTACTATAGAAGCAATTATATTTTAGGAGCGAGGGATTAGTGTAAAAGAACGACAACAAAAGCCACTGGATTAATTTTCTTAATTCCTATGAGC

Reverse complement sequence

GCTCATAGGAATTAAGAAAATTAATCCAGTGGCTTTTGTTGTCGTTCTTTTACACTAATCCCTCGCTCCTAAAATATAATTGCTTCTATAGTACTCCCTC[T/C]
GTTCCATAATATAAGGGATTTTGAGTTTTTGCTTGTACTGTTTGACCACTCGTCTTATTCAAAAAATTTACCGGTGAGTAGGTAGCATTTTATTTACCAA

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 83.70% 14.80% 1.50% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 51.20% 44.20% 4.63% 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 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 20.90% 74.30% 4.82% 0.00% NA
Tropical Japonica  504 90.10% 5.80% 4.17% 0.00% NA
Japonica Intermediate  241 66.40% 28.60% 4.98% 0.00% NA
VI/Aromatic  96 79.20% 20.80% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0621183896 A -> G LOC_Os06g36180.1 upstream_gene_variant ; 1004.0bp to feature; MODIFIER silent_mutation Average:34.727; most accessible tissue: Minghui63 root, score: 57.225 N N N N
vg0621183896 A -> G LOC_Os06g36170-LOC_Os06g36180 intergenic_region ; MODIFIER silent_mutation Average:34.727; most accessible tissue: Minghui63 root, score: 57.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621183896 NA 2.59E-11 mr1182 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
vg0621183896 5.22E-08 NA mr1768_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
vg0621183896 4.83E-07 NA mr1829_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
vg0621183896 5.14E-07 NA mr1842_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
vg0621183896 NA 5.97E-06 mr1866_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