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Detailed information for vg0618973254:

Variant ID: vg0618973254 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18973254
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGCACTGACTAGATGCACCTAATAGGTGTAGCCCCTGACTATGTGCTTAGTTGAACAAACTAAACATATAGTCAAGGAGTAAATAATCCAACCAACCGA[G/A]
TGGTTTTGATAATTGTAGTCAACCAAGTGACTTAATATTAAGATGTAGCATATGCGGTGTGAATCCCCGAGTAATCATGATATACCGACTGCTTTGTAAA

Reverse complement sequence

TTTACAAAGCAGTCGGTATATCATGATTACTCGGGGATTCACACCGCATATGCTACATCTTAATATTAAGTCACTTGGTTGACTACAATTATCAAAACCA[C/T]
TCGGTTGGTTGGATTATTTACTCCTTGACTATATGTTTAGTTTGTTCAACTAAGCACATAGTCAGGGGCTACACCTATTAGGTGCATCTAGTCAGTGCAC

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	91.60%	0.30%	2.26%	5.82%	NA
All Indica	2759	99.50%	0.00%	0.11%	0.43%	NA
All Japonica	1512	80.80%	0.40%	1.46%	17.39%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.30%	0.00%	0.00%	1.68%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.00%	0.22%	0.00%	NA
Indica Intermediate	786	99.60%	0.00%	0.13%	0.25%	NA
Temperate Japonica	767	70.90%	0.50%	0.78%	27.77%	NA
Tropical Japonica	504	96.80%	0.20%	0.99%	1.98%	NA
Japonica Intermediate	241	78.40%	0.40%	4.56%	16.60%	NA
VI/Aromatic	96	15.60%	8.30%	76.04%	0.00%	NA
Intermediate	90	88.90%	1.10%	10.00%	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
vg0618973254	G -> A	LOC_Os06g32630.1	downstream_gene_variant ; 2816.0bp to feature; MODIFIER	silent_mutation	Average:44.138; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg0618973254	G -> A	LOC_Os06g32610-LOC_Os06g32630	intergenic_region ; MODIFIER	silent_mutation	Average:44.138; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg0618973254	G -> DEL	N	N	silent_mutation	Average:44.138; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618973254	NA	4.33E-06	mr1057	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
vg0618973254	NA	2.62E-06	mr1565	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
vg0618973254	NA	8.46E-06	mr1884	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
vg0618973254	1.70E-06	NA	mr1024_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
vg0618973254	1.70E-06	1.70E-06	mr1024_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
vg0618973254	NA	2.66E-09	mr1057_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
vg0618973254	1.26E-06	1.70E-09	mr1565_2	Jap_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
vg0618973254	NA	3.92E-07	mr1585_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
vg0618973254	NA	1.03E-10	mr1829_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