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Detailed information for vg0515672827:

Variant ID: vg0515672827 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 15672827
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGCTCGGTCTGACGGAATACGGCTCCATCGGCTCTGTATCGGCCATCCCGAGCAGCACCATCTCGGCCTCCAGGGGGCCGGTCTGACCGCGCAAGTGCC[G/A]
CCGGTCAGACCGGCCTTATGCTCCGGTCAGACCGCCTTCTTGCGGCCGGTCAGACCAGCCAGGGCACGCCGGTCAGACCGCCACTATGTGGCTGGTCTGA

Reverse complement sequence

TCAGACCAGCCACATAGTGGCGGTCTGACCGGCGTGCCCTGGCTGGTCTGACCGGCCGCAAGAAGGCGGTCTGACCGGAGCATAAGGCCGGTCTGACCGG[C/T]
GGCACTTGCGCGGTCAGACCGGCCCCCTGGAGGCCGAGATGGTGCTGCTCGGGATGGCCGATACAGAGCCGATGGAGCCGTATTCCGTCAGACCGAGCCG

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	85.80%	6.10%	7.60%	0.55%	NA
All Indica	2759	93.00%	2.20%	4.31%	0.51%	NA
All Japonica	1512	74.10%	12.20%	12.90%	0.79%	NA
Aus	269	98.90%	0.70%	0.37%	0.00%	NA
Indica I	595	98.20%	1.00%	0.84%	0.00%	NA
Indica II	465	85.60%	3.70%	8.82%	1.94%	NA
Indica III	913	91.00%	2.70%	6.02%	0.22%	NA
Indica Intermediate	786	95.70%	1.70%	2.29%	0.38%	NA
Temperate Japonica	767	86.20%	6.50%	6.52%	0.78%	NA
Tropical Japonica	504	66.30%	15.10%	18.65%	0.00%	NA
Japonica Intermediate	241	51.90%	24.50%	21.16%	2.49%	NA
VI/Aromatic	96	30.20%	28.10%	41.67%	0.00%	NA
Intermediate	90	82.20%	13.30%	4.44%	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
vg0515672827	G -> DEL	N	N	silent_mutation	Average:33.958; most accessible tissue: Zhenshan97 root, score: 50.453	N	N	N	N
vg0515672827	G -> A	LOC_Os05g26970.1	upstream_gene_variant ; 1208.0bp to feature; MODIFIER	silent_mutation	Average:33.958; most accessible tissue: Zhenshan97 root, score: 50.453	N	N	N	N
vg0515672827	G -> A	LOC_Os05g26970-LOC_Os05g26980	intergenic_region ; MODIFIER	silent_mutation	Average:33.958; most accessible tissue: Zhenshan97 root, score: 50.453	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0515672827	NA	5.20E-06	mr1240_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
vg0515672827	1.22E-07	2.55E-09	mr1622_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
vg0515672827	9.30E-07	NA	mr1778_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