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Detailed information for vg1105900588:

Variant ID: vg1105900588 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5900588
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, G: 0.06, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

GAACCCATTTGATTTCTCATTATGTGTGAGAAGTACATCGGTGAGTTGCGGTATATAATGCCCTGAATTATTCGCCAATCAGTCAAAGTGCACGACAGAA[T/G]
TTAAACATTTAAATGTGAAATAAGACTCAGGAATACTCTCTGACCTGCATAGCTCTCTCCACTAAGAAGTAGCCCTCTTGACCTGTATTCAGGGAACTTC

Reverse complement sequence

GAAGTTCCCTGAATACAGGTCAAGAGGGCTACTTCTTAGTGGAGAGAGCTATGCAGGTCAGAGAGTATTCCTGAGTCTTATTTCACATTTAAATGTTTAA[A/C]
TTCTGTCGTGCACTTTGACTGATTGGCGAATAATTCAGGGCATTATATACCGCAACTCACCGATGTACTTCTCACACATAATGAGAAATCAAATGGGTTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.40%	13.50%	0.08%	0.00%	NA
All Indica	2759	82.30%	17.70%	0.04%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.07%	0.00%	NA
Aus	269	51.70%	48.00%	0.37%	0.00%	NA
Indica I	595	77.00%	22.90%	0.17%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	73.30%	26.70%	0.00%	0.00%	NA
Indica Intermediate	786	87.70%	12.30%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	88.90%	10.00%	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
vg1105900588	T -> G	LOC_Os11g10740.1	downstream_gene_variant ; 3812.0bp to feature; MODIFIER	silent_mutation	Average:63.08; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg1105900588	T -> G	LOC_Os11g10750.1	intron_variant ; MODIFIER	silent_mutation	Average:63.08; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105900588	NA	2.37E-06	mr1042	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
vg1105900588	NA	5.70E-09	mr1042	Ind_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
vg1105900588	NA	1.77E-06	mr1043	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
vg1105900588	2.49E-06	2.03E-09	mr1043	Ind_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
vg1105900588	NA	3.53E-06	mr1282	Ind_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
vg1105900588	NA	1.16E-07	mr1912	Ind_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
vg1105900588	8.95E-07	4.42E-08	mr1043_2	Ind_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
vg1105900588	NA	6.50E-07	mr1330_2	Ind_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
vg1105900588	NA	2.16E-07	mr1378_2	Ind_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
vg1105900588	NA	2.42E-06	mr1743_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