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Detailed information for vg0902343614:

Variant ID: vg0902343614 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 2343614
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


CTAGGCGCCGTATCCCTAAAGACACAGCAATCCTAAATCCATGAAGTAATGCTTCATACTCAGCTACATTATGGGACGCTGAAAAATGAATCCACAACAC[A/G]
TAGCTAAGCTGCTCTCCAGTCGGGGAAATTAATACAACCCCAGCCCAGTGCCTGAAATTCTTTTCGACCCGTCGAAATGCATAGTCCAGTACTCCAAGTT

Reverse complement sequence

AACTTGGAGTACTGGACTATGCATTTCGACGGGTCGAAAAGAATTTCAGGCACTGGGCTGGGGTTGTATTAATTTCCCCGACTGGAGAGCAGCTTAGCTA[T/C]
GTGTTGTGGATTCATTTTTCAGCGTCCCATAATGTAGCTGAGTATGAAGCATTACTTCATGGATTTAGGATTGCTGTGTCTTTAGGGATACGGCGCCTAG

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 82.20% 8.70% 4.36% 4.72% NA
All Indica  2759 97.00% 0.10% 0.65% 2.21% NA
All Japonica  1512 52.30% 26.50% 11.64% 9.52% NA
Aus  269 95.50% 0.00% 0.00% 4.46% NA
Indica I  595 98.30% 0.20% 0.67% 0.84% NA
Indica II  465 96.30% 0.00% 0.00% 3.66% NA
Indica III  913 96.80% 0.10% 0.66% 2.41% NA
Indica Intermediate  786 96.70% 0.10% 1.02% 2.16% NA
Temperate Japonica  767 42.50% 47.10% 10.17% 0.26% NA
Tropical Japonica  504 60.70% 1.20% 14.68% 23.41% NA
Japonica Intermediate  241 66.00% 14.10% 9.96% 9.96% NA
VI/Aromatic  96 95.80% 0.00% 1.04% 3.12% NA
Intermediate  90 75.60% 8.90% 12.22% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0902343614 A -> G LOC_Os09g04420.1 intron_variant ; MODIFIER silent_mutation Average:58.65; most accessible tissue: Zhenshan97 young leaf, score: 76.099 N N N N
vg0902343614 A -> DEL N N silent_mutation Average:58.65; most accessible tissue: Zhenshan97 young leaf, score: 76.099 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0902343614 NA 1.75E-06 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
vg0902343614 NA 3.20E-08 mr1010_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
vg0902343614 NA 4.16E-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
vg0902343614 1.74E-06 1.26E-07 mr1206_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
vg0902343614 NA 1.47E-07 mr1206_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
vg0902343614 2.82E-06 1.47E-10 mr1229_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
vg0902343614 NA 8.61E-09 mr1229_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
vg0902343614 NA 6.54E-08 mr1252_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
vg0902343614 NA 2.78E-06 mr1263_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
vg0902343614 NA 3.73E-08 mr1555_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
vg0902343614 NA 3.19E-06 mr1555_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
vg0902343614 1.39E-07 1.13E-09 mr1596_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
vg0902343614 NA 8.97E-09 mr1596_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
vg0902343614 NA 3.37E-08 mr1763_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
vg0902343614 NA 4.25E-06 mr1763_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
vg0902343614 3.25E-07 4.11E-12 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
vg0902343614 NA 2.20E-10 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