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Detailed information for vg1218852237:

Variant ID: vg1218852237 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18852237
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.70, G: 0.30, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

AGCGAAGCTCATGGACGGTGGTGTGCTGGAGCTCGCACCTGCTGATGGTGGCGATGTGGAGGGTATAAGAGAATCGGAAGAGGGATACCGGTGGAGGAGG[A/G]
GGCGGCGATGGTGGCGGCGGCGCACCGCCGCGGTTGCTGAGGAACTCGAGCTCCTGAAGGTTGTCGACGGCGGCGGATCGGAGCCAGGTATCCACGGTGT

Reverse complement sequence

ACACCGTGGATACCTGGCTCCGATCCGCCGCCGTCGACAACCTTCAGGAGCTCGAGTTCCTCAGCAACCGCGGCGGTGCGCCGCCGCCACCATCGCCGCC[T/C]
CCTCCTCCACCGGTATCCCTCTTCCGATTCTCTTATACCCTCCACATCGCCACCATCAGCAGGTGCGAGCTCCAGCACACCACCGTCCATGAGCTTCGCT

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	59.90%	37.30%	0.15%	2.58%	NA
All Indica	2759	66.50%	28.90%	0.22%	4.39%	NA
All Japonica	1512	56.00%	44.00%	0.00%	0.07%	NA
Aus	269	16.00%	84.00%	0.00%	0.00%	NA
Indica I	595	75.30%	24.20%	0.34%	0.17%	NA
Indica II	465	65.40%	15.90%	0.22%	18.49%	NA
Indica III	913	65.80%	33.20%	0.33%	0.66%	NA
Indica Intermediate	786	61.50%	35.00%	0.00%	3.56%	NA
Temperate Japonica	767	35.50%	64.50%	0.00%	0.00%	NA
Tropical Japonica	504	91.10%	8.90%	0.00%	0.00%	NA
Japonica Intermediate	241	47.70%	51.90%	0.00%	0.41%	NA
VI/Aromatic	96	64.60%	35.40%	0.00%	0.00%	NA
Intermediate	90	51.10%	47.80%	1.11%	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
vg1218852237	A -> DEL	LOC_Os12g31340.1	N	frameshift_variant	Average:76.541; most accessible tissue: Zhenshan97 young leaf, score: 88.127	N	N	N	N
vg1218852237	A -> G	LOC_Os12g31340.1	synonymous_variant ; p.Pro174Pro; LOW	synonymous_codon	Average:76.541; most accessible tissue: Zhenshan97 young leaf, score: 88.127	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218852237	NA	6.20E-10	mr1457	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
vg1218852237	NA	6.35E-07	mr1457	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
vg1218852237	6.28E-07	NA	mr1458	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
vg1218852237	NA	3.73E-14	mr1458	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
vg1218852237	NA	8.19E-06	mr1548	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
vg1218852237	NA	4.01E-07	mr1617	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
vg1218852237	NA	4.60E-06	mr1729	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
vg1218852237	NA	1.88E-07	mr1912	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
vg1218852237	2.61E-07	NA	mr1457_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
vg1218852237	NA	2.09E-06	mr1457_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
vg1218852237	NA	9.32E-06	mr1457_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
vg1218852237	3.85E-09	NA	mr1458_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
vg1218852237	NA	1.09E-11	mr1458_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
vg1218852237	NA	1.70E-06	mr1458_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