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Detailed information for vg0400744237:

Variant ID: vg0400744237 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 744237
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, C: 0.33, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

TGGAGCCAATGAGGTCGACAAGAAGGATGTATAGAGCTATCTCTGATCTCATCAACTTCCTATTCGAGGAAGAAAACTACCCTGTCGTTGACTATGTGCG[G/C]
TGTTCCATGCTGCCAAGTCGACGACAACTAGATAGGTTATCTTAAATATTGTGCTTGTGTGATTTTGATGAATAAGAGCAAGACCGGTTTCGGCTAACAG

Reverse complement sequence

CTGTTAGCCGAAACCGGTCTTGCTCTTATTCATCAAAATCACACAAGCACAATATTTAAGATAACCTATCTAGTTGTCGTCGACTTGGCAGCATGGAACA[C/G]
CGCACATAGTCAACGACAGGGTAGTTTTCTTCCTCGAATAGGAAGTTGATGAGATCAGAGATAGCTCTATACATCCTTCTTGTCGACCTCATTGGCTCCA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.40%	17.80%	0.74%	18.07%	NA
All Indica	2759	70.10%	19.80%	0.83%	9.24%	NA
All Japonica	1512	43.30%	17.70%	0.73%	38.36%	NA
Aus	269	95.90%	4.10%	0.00%	0.00%	NA
Indica I	595	91.90%	6.40%	0.17%	1.51%	NA
Indica II	465	67.50%	21.30%	0.65%	10.54%	NA
Indica III	913	59.30%	27.50%	0.88%	12.38%	NA
Indica Intermediate	786	67.80%	20.10%	1.40%	10.69%	NA
Temperate Japonica	767	63.10%	27.80%	0.26%	8.87%	NA
Tropical Japonica	504	22.20%	1.40%	1.19%	75.20%	NA
Japonica Intermediate	241	24.10%	19.50%	1.24%	55.19%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	64.40%	17.80%	1.11%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0400744237	G -> C	LOC_Os04g02180-LOC_Os04g02200	intergenic_region ; MODIFIER	silent_mutation	Average:54.879; most accessible tissue: Zhenshan97 young leaf, score: 78.938	N	N	N	N
vg0400744237	G -> DEL	N	N	silent_mutation	Average:54.879; most accessible tissue: Zhenshan97 young leaf, score: 78.938	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400744237	NA	8.55E-06	mr1192	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
vg0400744237	1.40E-07	NA	mr1613_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
vg0400744237	7.54E-06	NA	mr1962_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