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Detailed information for vg0136579184:

Variant ID: vg0136579184 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 36579184
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGTGACTGTGCGACTCGCACAATCGATGGCTCCCTTAAACTTGGTTAGCCAATCCATCCCAAGAATGACATCTAGGTCTTTGGATTCGAGAAGAATGAG[G/A]
TTGGCTAGAAATGGTGATCTTTGAATTTCTATTGTGATAGAAGGGCTGAATTGTACCGAAGTGGAACTATTCCCCGGGGTATGAACCCGCATGGGTGTGC

Reverse complement sequence

GCACACCCATGCGGGTTCATACCCCGGGGAATAGTTCCACTTCGGTACAATTCAGCCCTTCTATCACAATAGAAATTCAAAGATCACCATTTCTAGCCAA[C/T]
CTCATTCTTCTCGAATCCAAAGACCTAGATGTCATTCTTGGGATGGATTGGCTAACCAAGTTTAAGGGAGCCATCGATTGTGCGAGTCGCACAGTCACCT

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	49.40%	5.10%	3.17%	42.32%	NA
All Indica	2759	19.30%	8.30%	4.75%	67.67%	NA
All Japonica	1512	98.30%	0.10%	0.13%	1.52%	NA
Aus	269	83.30%	4.10%	4.46%	8.18%	NA
Indica I	595	19.50%	1.00%	3.36%	76.13%	NA
Indica II	465	17.00%	30.10%	8.60%	44.30%	NA
Indica III	913	13.90%	1.60%	2.96%	81.49%	NA
Indica Intermediate	786	26.80%	8.50%	5.60%	59.03%	NA
Temperate Japonica	767	99.00%	0.00%	0.13%	0.91%	NA
Tropical Japonica	504	97.60%	0.20%	0.20%	1.98%	NA
Japonica Intermediate	241	97.50%	0.00%	0.00%	2.49%	NA
VI/Aromatic	96	33.30%	0.00%	3.12%	63.54%	NA
Intermediate	90	64.40%	3.30%	2.22%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0136579184	G -> A	LOC_Os01g63120.1	synonymous_variant ; p.Asn471Asn; LOW	synonymous_codon	Average:7.909; most accessible tissue: Callus, score: 33.104	N	N	N	N
vg0136579184	G -> DEL	LOC_Os01g63120.1	N	frameshift_variant	Average:7.909; most accessible tissue: Callus, score: 33.104	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0136579184	NA	2.16E-06	mr1168_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
vg0136579184	NA	3.85E-10	mr1322_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
vg0136579184	NA	2.14E-09	mr1322_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
vg0136579184	NA	6.11E-06	mr1323_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
vg0136579184	NA	2.80E-06	mr1325_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
vg0136579184	NA	4.60E-07	mr1326_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
vg0136579184	NA	5.53E-08	mr1336_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
vg0136579184	NA	3.26E-10	mr1338_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
vg0136579184	NA	1.97E-06	mr1338_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
vg0136579184	NA	8.44E-09	mr1449_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
vg0136579184	NA	7.90E-08	mr1449_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
vg0136579184	NA	4.90E-08	mr1540_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
vg0136579184	NA	5.18E-08	mr1732_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
vg0136579184	NA	8.39E-06	mr1899_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