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Detailed information for vg1001300052:

Variant ID: vg1001300052 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1300052
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

ACCATTAAATATAACCATAATTGGTAGTGTAGTATGAATCACCCCATTAATGAGCTAATATTTCTAAGCATGACTAAGCATCTATAATAATCATATAGCT[G/A]
AACCAAACCAATATATAAGGTTCTAGCTAATCAAATTATAACCCATAGGAAAATAAAGTTATCTTCGGCCATAATTAAATGGGAAAGGCTCACCACCCGG

Reverse complement sequence

CCGGGTGGTGAGCCTTTCCCATTTAATTATGGCCGAAGATAACTTTATTTTCCTATGGGTTATAATTTGATTAGCTAGAACCTTATATATTGGTTTGGTT[C/T]
AGCTATATGATTATTATAGATGCTTAGTCATGCTTAGAAATATTAGCTCATTAATGGGGTGATTCATACTACACTACCAATTATGGTTATATTTAATGGT

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	42.10%	26.90%	12.31%	18.62%	NA
All Indica	2759	25.80%	44.10%	18.45%	11.63%	NA
All Japonica	1512	62.20%	2.20%	2.98%	32.61%	NA
Aus	269	93.70%	1.10%	1.49%	3.72%	NA
Indica I	595	17.00%	60.50%	7.73%	14.79%	NA
Indica II	465	19.60%	35.70%	30.75%	13.98%	NA
Indica III	913	33.80%	35.60%	21.14%	9.42%	NA
Indica Intermediate	786	26.80%	46.60%	16.16%	10.43%	NA
Temperate Japonica	767	87.20%	0.80%	1.96%	10.04%	NA
Tropical Japonica	504	33.50%	4.20%	4.37%	57.94%	NA
Japonica Intermediate	241	42.30%	2.90%	3.32%	51.45%	NA
VI/Aromatic	96	38.50%	3.10%	14.58%	43.75%	NA
Intermediate	90	56.70%	16.70%	11.11%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001300052	G -> A	LOC_Os10g03090.1	upstream_gene_variant ; 937.0bp to feature; MODIFIER	silent_mutation	Average:40.316; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg1001300052	G -> A	LOC_Os10g03080-LOC_Os10g03090	intergenic_region ; MODIFIER	silent_mutation	Average:40.316; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg1001300052	G -> DEL	N	N	silent_mutation	Average:40.316; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001300052	NA	6.40E-06	mr1011	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
vg1001300052	NA	2.81E-07	mr1206	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
vg1001300052	NA	4.99E-06	mr1236	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
vg1001300052	7.72E-08	NA	mr1486	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
vg1001300052	4.05E-06	2.87E-07	mr1486	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
vg1001300052	2.66E-08	NA	mr1548	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
vg1001300052	1.12E-06	7.89E-07	mr1548	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
vg1001300052	NA	4.53E-07	mr1570	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
vg1001300052	NA	6.88E-06	mr1634	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
vg1001300052	NA	1.84E-06	mr1727	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
vg1001300052	NA	5.46E-07	mr1763	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
vg1001300052	NA	2.48E-08	mr1770	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
vg1001300052	NA	1.57E-06	mr1858	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
vg1001300052	NA	1.58E-06	mr1859	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
vg1001300052	1.53E-06	6.12E-09	mr1486_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
vg1001300052	NA	5.11E-11	mr1728_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