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Detailed information for vg0804123286:

Variant ID: vg0804123286 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4123286
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCGGAATCACTTACCAACCTGCTAAACTTCATTCCATCTCTCTCATTCTAGGCTGGGTCCTCAACGTCACGTAGCATGTCTTGCAGCAGATCGTGATC[C/T]
ACATCAACCATTTCACCACCCAATGGAGAAGGTATAAGCATGTCATGCTCATCTTCATCTTCCTGATTATGTGCACCACTTCTGTCTGCTGCTGCTCCAC

Reverse complement sequence

GTGGAGCAGCAGCAGACAGAAGTGGTGCACATAATCAGGAAGATGAAGATGAGCATGACATGCTTATACCTTCTCCATTGGGTGGTGAAATGGTTGATGT[G/A]
GATCACGATCTGCTGCAAGACATGCTACGTGACGTTGAGGACCCAGCCTAGAATGAGAGAGATGGAATGAAGTTTAGCAGGTTGGTAAGTGATTCCGAGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.40%	3.20%	34.93%	4.49%	NA
All Indica	2759	35.10%	5.40%	54.48%	5.07%	NA
All Japonica	1512	95.30%	0.00%	0.79%	3.90%	NA
Aus	269	62.10%	0.00%	35.69%	2.23%	NA
Indica I	595	23.40%	3.50%	70.92%	2.18%	NA
Indica II	465	68.80%	3.40%	27.53%	0.22%	NA
Indica III	913	21.10%	8.10%	62.10%	8.65%	NA
Indica Intermediate	786	40.20%	4.70%	49.11%	5.98%	NA
Temperate Japonica	767	99.10%	0.00%	0.78%	0.13%	NA
Tropical Japonica	504	87.90%	0.00%	0.79%	11.31%	NA
Japonica Intermediate	241	98.80%	0.00%	0.83%	0.41%	NA
VI/Aromatic	96	78.10%	0.00%	17.71%	4.17%	NA
Intermediate	90	70.00%	1.10%	25.56%	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
vg0804123286	C -> T	LOC_Os08g07350.1	upstream_gene_variant ; 4908.0bp to feature; MODIFIER	silent_mutation	Average:30.748; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N
vg0804123286	C -> T	LOC_Os08g07370.1	downstream_gene_variant ; 3782.0bp to feature; MODIFIER	silent_mutation	Average:30.748; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N
vg0804123286	C -> T	LOC_Os08g07360.1	intron_variant ; MODIFIER	silent_mutation	Average:30.748; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N
vg0804123286	C -> DEL	N	N	silent_mutation	Average:30.748; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804123286	5.52E-07	NA	mr1526	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
vg0804123286	9.49E-07	NA	mr1526	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