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Detailed information for vg1219819590:

Variant ID: vg1219819590 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19819590
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.03, others allele: 0.00, population size: 168. )

Flanking Sequence (100 bp) in Reference Genome:

TTATTCTGACAAGTGTCCGAAGCCCCGACGCGTGAAGGTTGTCCTTGCACAGAACAACTCCACCGCACCAGCGTCAAAGGCTCGTATCAATCATGTTGCT[A/G]
CTGCAGAAGCCCAAGGTGCTCCAGATGTGATTTTGGGTACGTTCCCTGTTAACTCAGTTCCTGCAACAGTGCTTTTCGATTCTGGTGCTACATATTCCTT

Reverse complement sequence

AAGGAATATGTAGCACCAGAATCGAAAAGCACTGTTGCAGGAACTGAGTTAACAGGGAACGTACCCAAAATCACATCTGGAGCACCTTGGGCTTCTGCAG[T/C]
AGCAACATGATTGATACGAGCCTTTGACGCTGGTGCGGTGGAGTTGTTCTGTGCAAGGACAACCTTCACGCGTCGGGGCTTCGGACACTTGTCAGAATAA

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	92.40%	2.80%	1.86%	3.00%	NA
All Indica	2759	95.00%	2.00%	2.39%	0.69%	NA
All Japonica	1512	92.10%	0.30%	0.53%	7.08%	NA
Aus	269	66.50%	23.40%	4.46%	5.58%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	97.80%	1.90%	0.22%	0.00%	NA
Indica III	913	93.20%	2.30%	3.72%	0.77%	NA
Indica Intermediate	786	91.60%	2.90%	3.94%	1.53%	NA
Temperate Japonica	767	87.20%	0.10%	0.91%	11.73%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	91.70%	0.80%	0.41%	7.05%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	93.30%	3.30%	2.22%	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
vg1219819590	A -> DEL	LOC_Os12g32800.1	N	frameshift_variant	Average:18.004; most accessible tissue: Zhenshan97 flag leaf, score: 23.298	N	N	N	N
vg1219819590	A -> G	LOC_Os12g32800.1	missense_variant ; p.Thr682Ala; MODERATE	nonsynonymous_codon ; T682A	Average:18.004; most accessible tissue: Zhenshan97 flag leaf, score: 23.298	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219819590	1.13E-06	NA	mr1632	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