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Detailed information for vg0519823381:

Variant ID: vg0519823381 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 19823381
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

AATCACAAATATCGAACGCCTCCACTCAATGTTAGTAGTACATGTGTTATACTGTGATTTTTTTTTCTTGTGCTCAGGTGCACCTACGGGTGATGTATAC[G/A]
CTTATAACAACTTTATTTTAAAACTTTAAACAACTTTTTTTTTCTGTTTTACTTATCTGGTCAATAATTTGATCGTACTATTTGATTCGTTACAATTAAA

Reverse complement sequence

TTTAATTGTAACGAATCAAATAGTACGATCAAATTATTGACCAGATAAGTAAAACAGAAAAAAAAAGTTGTTTAAAGTTTTAAAATAAAGTTGTTATAAG[C/T]
GTATACATCACCCGTAGGTGCACCTGAGCACAAGAAAAAAAAATCACAGTATAACACATGTACTACTAACATTGAGTGGAGGCGTTCGATATTTGTGATT

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	75.50%	23.90%	0.30%	0.30%	NA
All Indica	2759	60.10%	39.00%	0.43%	0.47%	NA
All Japonica	1512	99.00%	1.00%	0.00%	0.00%	NA
Aus	269	91.10%	8.60%	0.37%	0.00%	NA
Indica I	595	40.20%	59.20%	0.34%	0.34%	NA
Indica II	465	59.80%	39.10%	0.65%	0.43%	NA
Indica III	913	67.10%	31.90%	0.22%	0.77%	NA
Indica Intermediate	786	67.20%	31.90%	0.64%	0.25%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	14.40%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0519823381	G -> DEL	N	N	silent_mutation	Average:60.925; most accessible tissue: Zhenshan97 root, score: 82.912	N	N	N	N
vg0519823381	G -> A	LOC_Os05g33680-LOC_Os05g33690	intergenic_region ; MODIFIER	silent_mutation	Average:60.925; most accessible tissue: Zhenshan97 root, score: 82.912	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0519823381	8.66E-06	1.98E-07	mr1201_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
vg0519823381	NA	2.08E-07	mr1201_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
vg0519823381	5.61E-06	3.21E-06	mr1219_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
vg0519823381	NA	5.06E-08	mr1219_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
vg0519823381	NA	2.25E-06	mr1274_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
vg0519823381	NA	4.52E-09	mr1322_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