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Detailed information for vg0401249964:

Variant ID: vg0401249964 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1249964
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTTCATGTGATGAAAAAAAATCACCACACAAAATGTTTAGCAGGTAATATGTGCAGGAGAACTACATGCTCATGTGTATATATGCGTTGATTGACAAAA[A/G]
TATAGAGAGTAGGATTTGATCTATCACTAAATACATTACTACGTACATATATCTAGGGATAAAAATGGTCGGAAAAAAGCCTGGGTAAAATTAGTAAAAA

Reverse complement sequence

TTTTTACTAATTTTACCCAGGCTTTTTTCCGACCATTTTTATCCCTAGATATATGTACGTAGTAATGTATTTAGTGATAGATCAAATCCTACTCTCTATA[T/C]
TTTTGTCAATCAACGCATATATACACATGAGCATGTAGTTCTCCTGCACATATTACCTGCTAAACATTTTGTGTGGTGATTTTTTTTCATCACATGAAGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.90%	28.90%	0.19%	0.00%	NA
All Indica	2759	85.10%	14.70%	0.22%	0.00%	NA
All Japonica	1512	39.40%	60.60%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.80%	2.20%	0.00%	0.00%	NA
Indica II	465	77.40%	22.40%	0.22%	0.00%	NA
Indica III	913	79.50%	20.40%	0.11%	0.00%	NA
Indica Intermediate	786	86.50%	13.00%	0.51%	0.00%	NA
Temperate Japonica	767	55.50%	44.30%	0.13%	0.00%	NA
Tropical Japonica	504	18.30%	81.70%	0.00%	0.00%	NA
Japonica Intermediate	241	32.00%	68.00%	0.00%	0.00%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	66.70%	31.10%	2.22%	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
vg0401249964	A -> G	LOC_Os04g03040.1	upstream_gene_variant ; 4037.0bp to feature; MODIFIER	silent_mutation	Average:40.169; most accessible tissue: Callus, score: 76.694	N	N	N	N
vg0401249964	A -> G	LOC_Os04g03050.1	intron_variant ; MODIFIER	silent_mutation	Average:40.169; most accessible tissue: Callus, score: 76.694	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401249964	NA	5.54E-09	mr1182	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
vg0401249964	NA	3.65E-08	mr1282	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
vg0401249964	NA	3.31E-06	mr1648	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
vg0401249964	2.23E-06	NA	mr1650	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
vg0401249964	9.59E-06	1.43E-08	mr1650	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
vg0401249964	NA	2.26E-07	mr1658	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
vg0401249964	NA	3.25E-07	mr1182_2	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
vg0401249964	NA	2.27E-06	mr1195_2	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
vg0401249964	NA	1.02E-06	mr1282_2	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
vg0401249964	NA	2.04E-06	mr1474_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
vg0401249964	NA	7.55E-06	mr1539_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
vg0401249964	NA	3.92E-06	mr1540_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
vg0401249964	NA	7.66E-07	mr1566_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
vg0401249964	NA	9.22E-06	mr1566_2	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
vg0401249964	NA	3.39E-07	mr1749_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