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Detailed information for vg1118218762:

Variant ID: vg1118218762 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18218762
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTGGCAAAGGATACTTGTTCTTGATGGTGACCTCATTGAGTGCGCGGTAGTCAACGCACATCCTCTTGGTTTTGTCTTTCTTCTCCACAAAGATAACC[A/G]
GAGCACCCCAAGGTGACGTGCTCGGGCGGATGTATCCCAAGGTAACTGTTCATCGACTTGTTTCTTGACTTCCGCCAACTCGTTGGCTCCCATTCTGTAA

Reverse complement sequence

TTACAGAATGGGAGCCAACGAGTTGGCGGAAGTCAAGAAACAAGTCGATGAACAGTTACCTTGGGATACATCCGCCCGAGCACGTCACCTTGGGGTGCTC[T/C]
GGTTATCTTTGTGGAGAAGAAAGACAAAACCAAGAGGATGTGCGTTGACTACCGCGCACTCAATGAGGTCACCATCAAGAACAAGTATCCTTTGCCAAGG

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	16.50%	4.20%	16.46%	62.89%	NA
All Indica	2759	5.40%	5.00%	17.25%	72.38%	NA
All Japonica	1512	38.30%	3.30%	12.43%	45.97%	NA
Aus	269	4.50%	1.50%	18.22%	75.84%	NA
Indica I	595	2.20%	17.00%	14.45%	66.39%	NA
Indica II	465	10.30%	0.90%	10.75%	78.06%	NA
Indica III	913	3.00%	0.30%	21.36%	75.36%	NA
Indica Intermediate	786	7.60%	3.80%	18.45%	70.10%	NA
Temperate Japonica	767	61.10%	5.50%	5.48%	27.90%	NA
Tropical Japonica	504	3.00%	1.20%	22.02%	73.81%	NA
Japonica Intermediate	241	39.40%	0.80%	14.52%	45.23%	NA
VI/Aromatic	96	29.20%	3.10%	46.88%	20.83%	NA
Intermediate	90	13.30%	2.20%	22.22%	62.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1118218762	A -> DEL	N	N	silent_mutation	Average:18.825; most accessible tissue: Minghui63 young leaf, score: 43.347	N	N	N	N
vg1118218762	A -> G	LOC_Os11g31240.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:18.825; most accessible tissue: Minghui63 young leaf, score: 43.347	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118218762	NA	4.93E-06	mr1961_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