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Detailed information for vg1110034297:

Variant ID: vg1110034297 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10034297
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.89, G: 0.11, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

GGTCAAACATCAAAGCAATCGGAGCCATCAACCATACCAACTCCATATAAACCTCCGGTTGTGATGCCATGGTATCCATATCCAATGTCACTATATGGTT[G/A]
TCCTTTTATGTATTACATGCCTTGGATGCATCAGCCACCTATGCCGTATTACCAAGAGTGGAAGGAATCACCTAGGTCAGCATCAAGTCATTCATCTAAC

Reverse complement sequence

GTTAGATGAATGACTTGATGCTGACCTAGGTGATTCCTTCCACTCTTGGTAATACGGCATAGGTGGCTGATGCATCCAAGGCATGTAATACATAAAAGGA[C/T]
AACCATATAGTGACATTGGATATGGATACCATGGCATCACAACCGGAGGTTTATATGGAGTTGGTATGGTTGATGGCTCCGATTGCTTTGATGTTTGACC

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	41.90%	10.90%	18.98%	28.27%	NA
All Indica	2759	22.50%	13.20%	29.32%	34.90%	NA
All Japonica	1512	81.70%	4.00%	1.32%	12.96%	NA
Aus	269	21.60%	1.90%	23.05%	53.53%	NA
Indica I	595	41.50%	9.70%	13.11%	35.63%	NA
Indica II	465	22.40%	5.40%	33.33%	38.92%	NA
Indica III	913	3.50%	24.00%	40.64%	31.87%	NA
Indica Intermediate	786	30.40%	8.00%	26.08%	35.50%	NA
Temperate Japonica	767	73.50%	4.80%	2.22%	19.43%	NA
Tropical Japonica	504	94.20%	2.80%	0.60%	2.38%	NA
Japonica Intermediate	241	81.30%	4.10%	0.00%	14.52%	NA
VI/Aromatic	96	19.80%	70.80%	1.04%	8.33%	NA
Intermediate	90	51.10%	15.60%	5.56%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110034297	G -> A	LOC_Os11g17900.1	downstream_gene_variant ; 4574.0bp to feature; MODIFIER	silent_mutation	Average:13.043; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg1110034297	G -> A	LOC_Os11g17890.1	intron_variant ; MODIFIER	silent_mutation	Average:13.043; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg1110034297	G -> DEL	N	N	silent_mutation	Average:13.043; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110034297	NA	4.56E-06	mr1062	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
vg1110034297	NA	3.44E-06	mr1143	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
vg1110034297	NA	9.37E-06	mr1535	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
vg1110034297	1.53E-06	1.53E-06	mr1726	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
vg1110034297	2.36E-06	2.36E-06	mr1950	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
vg1110034297	4.39E-06	7.28E-07	mr1995	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