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Detailed information for vg0112972548:

Variant ID: vg0112972548 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 12972548
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGACTGACTCGTTTTGAAAAACTCACTTTAAACGAGCGACCAAGATTTTCCCTTGAACCACCAGAACAGATCCCCATTTTCCCGGAACAAATCCAATTGC[G/A]
AAGAACATATGCAATGAAAAAGGATTCAGAGGGCTCTTAGGTTTTTCCATTTGGCTTGTCCTACGGTCAAGGTCGGCTCTGATACCAACTTGTCACGCCC

Reverse complement sequence

GGGCGTGACAAGTTGGTATCAGAGCCGACCTTGACCGTAGGACAAGCCAAATGGAAAAACCTAAGAGCCCTCTGAATCCTTTTTCATTGCATATGTTCTT[C/T]
GCAATTGGATTTGTTCCGGGAAAATGGGGATCTGTTCTGGTGGTTCAAGGGAAAATCTTGGTCGCTCGTTTAAAGTGAGTTTTTCAAAACGAGTCAGTCT

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	35.20%	0.80%	24.97%	39.06%	NA
All Indica	2759	6.50%	0.90%	31.64%	60.93%	NA
All Japonica	1512	82.50%	0.50%	12.24%	4.76%	NA
Aus	269	59.50%	0.40%	21.56%	18.59%	NA
Indica I	595	7.10%	0.30%	20.17%	72.44%	NA
Indica II	465	4.10%	1.30%	33.33%	61.29%	NA
Indica III	913	5.00%	1.90%	41.62%	51.48%	NA
Indica Intermediate	786	9.20%	0.10%	27.74%	62.98%	NA
Temperate Japonica	767	90.90%	0.10%	7.82%	1.17%	NA
Tropical Japonica	504	64.30%	1.00%	22.82%	11.90%	NA
Japonica Intermediate	241	94.20%	0.40%	4.15%	1.24%	NA
VI/Aromatic	96	28.10%	2.10%	47.92%	21.88%	NA
Intermediate	90	55.60%	0.00%	20.00%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0112972548	G -> A	LOC_Os01g23040.1	upstream_gene_variant ; 3632.0bp to feature; MODIFIER	silent_mutation	Average:8.331; most accessible tissue: Callus, score: 16.161	N	N	N	N
vg0112972548	G -> A	LOC_Os01g23050.1	upstream_gene_variant ; 24.0bp to feature; MODIFIER	silent_mutation	Average:8.331; most accessible tissue: Callus, score: 16.161	N	N	N	N
vg0112972548	G -> A	LOC_Os01g23060.1	upstream_gene_variant ; 1977.0bp to feature; MODIFIER	silent_mutation	Average:8.331; most accessible tissue: Callus, score: 16.161	N	N	N	N
vg0112972548	G -> A	LOC_Os01g23050-LOC_Os01g23060	intergenic_region ; MODIFIER	silent_mutation	Average:8.331; most accessible tissue: Callus, score: 16.161	N	N	N	N
vg0112972548	G -> DEL	N	N	silent_mutation	Average:8.331; most accessible tissue: Callus, score: 16.161	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112972548	NA	2.52E-10	mr1712	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
vg0112972548	6.61E-06	NA	mr1082_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
vg0112972548	NA	1.67E-06	mr1227_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
vg0112972548	NA	5.38E-06	mr1910_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
vg0112972548	NA	1.10E-08	mr1940_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