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Detailed information for vg0614982179:

Variant ID: vg0614982179 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14982179
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAACGACCAAGAGAAGGTTGTGTTTGCTACACACCAGCTGCAAGGTCCCGCTTCTGTTTGGTGGGACAACTACATGGTGACCTGTCCAGCTGGGACAGA[G/A]
GTTAGCTGGTCAGAGTTTTGTCAGAGTTTCAATAAGGCATAGGTTCCCGAGGGAATCATGGCACAAAAGAATAGAGAGTTCCGTTCTCTGCAACAAGGAA

Reverse complement sequence

TTCCTTGTTGCAGAGAACGGAACTCTCTATTCTTTTGTGCCATGATTCCCTCGGGAACCTATGCCTTATTGAAACTCTGACAAAACTCTGACCAGCTAAC[C/T]
TCTGTCCCAGCTGGACAGGTCACCATGTAGTTGTCCCACCAAACAGAAGCGGGACCTTGCAGCTGGTGTGTAGCAAACACAACCTTCTCTTGGTCGTTGC

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	39.40%	0.20%	7.83%	52.62%	NA
All Indica	2759	7.80%	0.20%	11.96%	80.07%	NA
All Japonica	1512	91.90%	0.00%	0.73%	7.41%	NA
Aus	269	70.60%	0.40%	4.09%	24.91%	NA
Indica I	595	9.90%	0.00%	11.60%	78.49%	NA
Indica II	465	5.60%	0.40%	13.55%	80.43%	NA
Indica III	913	5.00%	0.30%	9.97%	84.67%	NA
Indica Intermediate	786	10.60%	0.10%	13.61%	75.70%	NA
Temperate Japonica	767	96.70%	0.00%	0.39%	2.87%	NA
Tropical Japonica	504	83.90%	0.00%	1.39%	14.68%	NA
Japonica Intermediate	241	92.90%	0.00%	0.41%	6.64%	NA
VI/Aromatic	96	21.90%	1.00%	12.50%	64.58%	NA
Intermediate	90	52.20%	0.00%	6.67%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0614982179	G -> A	LOC_Os06g25630.1	upstream_gene_variant ; 2418.0bp to feature; MODIFIER	silent_mutation	Average:9.961; most accessible tissue: Callus, score: 53.467	N	N	N	N
vg0614982179	G -> A	LOC_Os06g25610.1	downstream_gene_variant ; 4390.0bp to feature; MODIFIER	silent_mutation	Average:9.961; most accessible tissue: Callus, score: 53.467	N	N	N	N
vg0614982179	G -> A	LOC_Os06g25620.1	intron_variant ; MODIFIER	silent_mutation	Average:9.961; most accessible tissue: Callus, score: 53.467	N	N	N	N
vg0614982179	G -> DEL	N	N	silent_mutation	Average:9.961; most accessible tissue: Callus, score: 53.467	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614982179	NA	8.00E-06	mr1346_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
vg0614982179	NA	5.12E-06	mr1428_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
vg0614982179	NA	8.32E-06	mr1428_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