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Detailed information for vg1124423034:

Variant ID: vg1124423034 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24423034
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 350. )

Flanking Sequence (100 bp) in Reference Genome:


AGCACTAGCAAGTGGGACAACTATTGGGATGATATAGGATTTCTTGTTTGTTTTGGATGATGTTGATGTGCAAAGTGGTAATTGCAGCATTGAAGACCCT[G/A]
TGCATAATTCCCTATTCCCTTGTACGAACACCTTACTTGAATTGCTAAATACACCATATGTAGGAACCATTCCCTCGAGATTGTTGAAGGATAAGTTGAG

Reverse complement sequence

CTCAACTTATCCTTCAACAATCTCGAGGGAATGGTTCCTACATATGGTGTATTTAGCAATTCAAGTAAGGTGTTCGTACAAGGGAATAGGGAATTATGCA[C/T]
AGGGTCTTCAATGCTGCAATTACCACTTTGCACATCAACATCATCCAAAACAAACAAGAAATCCTATATCATCCCAATAGTTGTCCCACTTGCTAGTGCT

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 98.20% 1.40% 0.42% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 94.60% 4.20% 1.19% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 89.70% 8.00% 2.35% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg1124423034 G -> A LOC_Os11g40810.1 missense_variant ; p.Thr350Ile; MODERATE nonsynonymous_codon ; T350I Average:40.296; most accessible tissue: Callus, score: 71.854 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124423034 4.66E-06 4.66E-06 mr1346 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
vg1124423034 1.35E-06 1.35E-06 mr1803 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
vg1124423034 NA 3.66E-06 mr1305_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
vg1124423034 NA 8.80E-07 mr1456_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
vg1124423034 NA 3.35E-06 mr1585_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
vg1124423034 NA 2.90E-06 mr1765_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