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Detailed information for vg0119898952:

Variant ID: vg0119898952 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 19898952
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

CATCTGAAGAAATTTCTTCAATTTCATCTTCAAAATCACTGTCATTATCACTTCCTACATCTTCTACATCTGAACTGTCTTCTTGTGCAACTTGTGTCTC[A/G]
ACATATATATCTGCAACCTCTGCTTCACTAGTACAGTCTGACATCAGTTGGCAAACATTATCGTCCAACAAAACACAAAGACCATCCTTCAGTTCTTTCA

Reverse complement sequence

TGAAAGAACTGAAGGATGGTCTTTGTGTTTTGTTGGACGATAATGTTTGCCAACTGATGTCAGACTGTACTAGTGAAGCAGAGGTTGCAGATATATATGT[T/C]
GAGACACAAGTTGCACAAGAAGACAGTTCAGATGTAGAAGATGTAGGAAGTGATAATGACAGTGATTTTGAAGATGAAATTGAAGAAATTTCTTCAGATG

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	84.00%	3.20%	6.09%	6.75%	NA
All Indica	2759	74.50%	5.10%	9.71%	10.73%	NA
All Japonica	1512	99.40%	0.10%	0.20%	0.33%	NA
Aus	269	87.00%	2.60%	4.83%	5.58%	NA
Indica I	595	89.90%	3.50%	3.19%	3.36%	NA
Indica II	465	74.20%	3.20%	12.47%	10.11%	NA
Indica III	913	62.10%	7.90%	11.83%	18.18%	NA
Indica Intermediate	786	77.40%	4.10%	10.56%	8.02%	NA
Temperate Japonica	767	99.30%	0.00%	0.13%	0.52%	NA
Tropical Japonica	504	99.40%	0.00%	0.40%	0.20%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	91.10%	2.20%	3.33%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0119898952	A -> G	LOC_Os01g35960.1	synonymous_variant ; p.Val101Val; LOW	synonymous_codon	Average:34.468; most accessible tissue: Minghui63 young leaf, score: 60.103	N	N	N	N
vg0119898952	A -> DEL	LOC_Os01g35960.1	N	frameshift_variant	Average:34.468; most accessible tissue: Minghui63 young leaf, score: 60.103	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0119898952	NA	3.34E-06	mr1511_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
vg0119898952	6.25E-06	NA	mr1739_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