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Detailed information for vg1002248885:

Variant ID: vg1002248885 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 2248885
Reference Allele: C	Alternative Allele: A,T
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTTAATATATGGTGCCGTTAACTTTTGAATATGTATTTTGACCATTCATTTGATTCAAAATTTTTATGCAAACATAGAAAAATATAAGTCACGCTTAA[C/A,T]
GAAACTTTAGTGATAAATCAAATAAAAAACAAATAATGATTATATGATTTTTTAATAAAATAAACAGTGAAGCGCGTATAAGAAAAAAATCAACAACGTG

Reverse complement sequence

CACGTTGTTGATTTTTTTCTTATACGCGCTTCACTGTTTATTTTATTAAAAAATCATATAATCATTATTTGTTTTTTATTTGATTTATCACTAAAGTTTC[G/T,A]
TTAAGCGTGACTTATATTTTTCTATGTTTGCATAAAAATTTTGAATCAAATGAATGGTCAAAATACATATTCAAAAGTTAACGGCACCATATATTAAAAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.70%	0.10%	1.38%	59.73%	T: 0.02%
All Indica	2759	16.90%	0.10%	0.69%	82.28%	NA
All Japonica	1512	84.10%	0.00%	0.26%	15.54%	T: 0.07%
Aus	269	13.80%	0.00%	4.46%	81.78%	NA
Indica I	595	33.80%	0.00%	0.34%	65.88%	NA
Indica II	465	3.70%	0.00%	0.43%	95.91%	NA
Indica III	913	17.70%	0.10%	0.55%	81.60%	NA
Indica Intermediate	786	11.10%	0.30%	1.27%	87.40%	NA
Temperate Japonica	767	90.90%	0.00%	0.26%	8.87%	NA
Tropical Japonica	504	78.00%	0.00%	0.20%	21.63%	T: 0.20%
Japonica Intermediate	241	75.50%	0.00%	0.41%	24.07%	NA
VI/Aromatic	96	15.60%	4.20%	29.17%	51.04%	NA
Intermediate	90	43.30%	0.00%	2.22%	54.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1002248885	C -> T	LOC_Os10g04700.1	upstream_gene_variant ; 2912.0bp to feature; MODIFIER	silent_mutation	Average:28.339; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N
vg1002248885	C -> T	LOC_Os10g04700.2	upstream_gene_variant ; 2912.0bp to feature; MODIFIER	silent_mutation	Average:28.339; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N
vg1002248885	C -> T	LOC_Os10g04710.1	downstream_gene_variant ; 361.0bp to feature; MODIFIER	silent_mutation	Average:28.339; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N
vg1002248885	C -> T	LOC_Os10g04720.1	downstream_gene_variant ; 495.0bp to feature; MODIFIER	silent_mutation	Average:28.339; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N
vg1002248885	C -> T	LOC_Os10g04710-LOC_Os10g04720	intergenic_region ; MODIFIER	silent_mutation	Average:28.339; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N
vg1002248885	C -> A	LOC_Os10g04700.1	upstream_gene_variant ; 2912.0bp to feature; MODIFIER	silent_mutation	Average:28.339; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N
vg1002248885	C -> A	LOC_Os10g04700.2	upstream_gene_variant ; 2912.0bp to feature; MODIFIER	silent_mutation	Average:28.339; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N
vg1002248885	C -> A	LOC_Os10g04710.1	downstream_gene_variant ; 361.0bp to feature; MODIFIER	silent_mutation	Average:28.339; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N
vg1002248885	C -> A	LOC_Os10g04720.1	downstream_gene_variant ; 495.0bp to feature; MODIFIER	silent_mutation	Average:28.339; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N
vg1002248885	C -> A	LOC_Os10g04710-LOC_Os10g04720	intergenic_region ; MODIFIER	silent_mutation	Average:28.339; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N
vg1002248885	C -> DEL	N	N	silent_mutation	Average:28.339; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1002248885	6.19E-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
vg1002248885	3.79E-08	5.41E-24	mr1548	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
vg1002248885	8.71E-06	NA	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
vg1002248885	NA	9.18E-20	mr1588	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
vg1002248885	NA	3.21E-06	mr1588	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
vg1002248885	NA	1.00E-06	mr1709	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
vg1002248885	2.94E-07	NA	mr1486_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
vg1002248885	5.31E-06	NA	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
vg1002248885	2.44E-06	NA	mr1588_2	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
vg1002248885	5.39E-07	2.14E-06	mr1588_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
vg1002248885	NA	1.38E-11	mr1709_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