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Detailed information for vg1123024327:

Variant ID: vg1123024327 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23024327
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTCACTGAGATAAATCCCTTTTTATATATGATAGACAGCAGATCACTGATCAAAGTTTCTTCAGATGATTAGGAAGTTTCTGTTATAAAACCGGCCCC[G/A]
AAATCACATTAGAAACAAAACGCGGAAGAAACACCATAGGAGATCTAAACATGAAGACGACACCGAGGCACGATATTTGATAACGGAGTGCAGCCGAGGC

Reverse complement sequence

GCCTCGGCTGCACTCCGTTATCAAATATCGTGCCTCGGTGTCGTCTTCATGTTTAGATCTCCTATGGTGTTTCTTCCGCGTTTTGTTTCTAATGTGATTT[C/T]
GGGGCCGGTTTTATAACAGAAACTTCCTAATCATCTGAAGAAACTTTGATCAGTGATCTGCTGTCTATCATATATAAAAAGGGATTTATCTCAGTGAAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.50%	1.40%	1.16%	6.94%	NA
All Indica	2759	87.80%	0.10%	1.20%	10.95%	NA
All Japonica	1512	93.70%	4.00%	1.39%	0.86%	NA
Aus	269	98.90%	0.00%	0.37%	0.74%	NA
Indica I	595	90.30%	0.00%	0.84%	8.91%	NA
Indica II	465	97.40%	0.00%	0.00%	2.58%	NA
Indica III	913	76.60%	0.00%	2.19%	21.25%	NA
Indica Intermediate	786	93.30%	0.30%	1.02%	5.47%	NA
Temperate Japonica	767	95.70%	2.70%	0.52%	1.04%	NA
Tropical Japonica	504	91.10%	5.40%	2.58%	0.99%	NA
Japonica Intermediate	241	92.90%	5.40%	1.66%	0.00%	NA
VI/Aromatic	96	92.70%	0.00%	0.00%	7.29%	NA
Intermediate	90	94.40%	1.10%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123024327	G -> A	LOC_Os11g38760.1	upstream_gene_variant ; 3958.0bp to feature; MODIFIER	silent_mutation	Average:33.064; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg1123024327	G -> A	LOC_Os11g38750-LOC_Os11g38760	intergenic_region ; MODIFIER	silent_mutation	Average:33.064; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg1123024327	G -> DEL	N	N	silent_mutation	Average:33.064; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123024327	NA	4.29E-07	mr1951	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
vg1123024327	7.95E-06	7.95E-06	mr1430_2	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