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Detailed information for vg0403818065:

Variant ID: vg0403818065 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3818065
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, A: 0.09, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTTGTCCCACGCTCCTCCACTTGCTACCCCTTTGGTCACCCTCATTCCCAGTGCCCCATTCTACCTCTCGCGGGGCAGCGCAAGAGTCGGATTTTGGC[C/A]
GAGCCTGGAATTGGAAGAGGAGCCGACAAGCACCATGGACAAACCATGAACCTAGGACGATCCATAAGCATGCCTTGCAGCCAACGCCGCAGCTGGGAGC

Reverse complement sequence

GCTCCCAGCTGCGGCGTTGGCTGCAAGGCATGCTTATGGATCGTCCTAGGTTCATGGTTTGTCCATGGTGCTTGTCGGCTCCTCTTCCAATTCCAGGCTC[G/T]
GCCAAAATCCGACTCTTGCGCTGCCCCGCGAGAGGTAGAATGGGGCACTGGGAATGAGGGTGACCAAAGGGGTAGCAAGTGGAGGAGCGTGGGACAAGAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.80%	34.30%	0.21%	5.71%	NA
All Indica	2759	88.40%	8.60%	0.07%	2.86%	NA
All Japonica	1512	5.90%	81.30%	0.40%	12.37%	NA
Aus	269	56.10%	42.00%	0.74%	1.12%	NA
Indica I	595	98.70%	1.30%	0.00%	0.00%	NA
Indica II	465	80.90%	14.00%	0.22%	4.95%	NA
Indica III	913	88.50%	7.70%	0.00%	3.83%	NA
Indica Intermediate	786	85.10%	12.10%	0.13%	2.67%	NA
Temperate Japonica	767	1.70%	96.60%	0.39%	1.30%	NA
Tropical Japonica	504	10.90%	59.70%	0.60%	28.77%	NA
Japonica Intermediate	241	8.70%	78.00%	0.00%	13.28%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	67.80%	31.10%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403818065	C -> DEL	LOC_Os04g07190.1	N	frameshift_variant	Average:45.544; most accessible tissue: Zhenshan97 flag leaf, score: 82.17	N	N	N	N
vg0403818065	C -> A	LOC_Os04g07190.1	missense_variant ; p.Arg220Leu; MODERATE	nonsynonymous_codon ; R220L	Average:45.544; most accessible tissue: Zhenshan97 flag leaf, score: 82.17	unknown	unknown	TOLERATED	0.06

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403818065	5.45E-06	NA	mr1315	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
vg0403818065	NA	3.37E-08	mr1993	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