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Detailed information for vg0128647202:

Variant ID: vg0128647202 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 28647202
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.03, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

ATATTACCTCTCTGTCATTTATTGGACAGATGGATGTGGAGCAACATGGTGATGGAGAGATGGCCGAAGAGGAAGAGGTTTTTGATGAAGGAAGCACATC[G/A]
TCAAGTGATGATGAGATTATTTCCATGTGCCGCAAGAATATGAACATGGCTCAAACTATGGTTGCTCAACTTGTCCCTATCCTTGGTATGTACTCCGAGC

Reverse complement sequence

GCTCGGAGTACATACCAAGGATAGGGACAAGTTGAGCAACCATAGTTTGAGCCATGTTCATATTCTTGCGGCACATGGAAATAATCTCATCATCACTTGA[C/T]
GATGTGCTTCCTTCATCAAAAACCTCTTCCTCTTCGGCCATCTCTCCATCACCATGTTGCTCCACATCCATCTGTCCAATAAATGACAGAGAGGTAATAT

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	77.60%	3.80%	3.64%	15.00%	NA
All Indica	2759	76.40%	0.90%	4.86%	17.83%	NA
All Japonica	1512	90.40%	0.00%	0.79%	8.80%	NA
Aus	269	32.70%	41.30%	4.46%	21.56%	NA
Indica I	595	89.10%	0.00%	3.70%	7.23%	NA
Indica II	465	55.50%	0.60%	12.04%	31.83%	NA
Indica III	913	76.70%	0.50%	1.64%	21.14%	NA
Indica Intermediate	786	78.80%	2.30%	5.22%	13.74%	NA
Temperate Japonica	767	99.60%	0.00%	0.13%	0.26%	NA
Tropical Japonica	504	74.00%	0.00%	1.59%	24.40%	NA
Japonica Intermediate	241	95.40%	0.00%	1.24%	3.32%	NA
VI/Aromatic	96	26.00%	37.50%	12.50%	23.96%	NA
Intermediate	90	87.80%	6.70%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0128647202	G -> A	LOC_Os01g49870.1	synonymous_variant ; p.Ser234Ser; LOW	synonymous_codon	Average:30.663; most accessible tissue: Callus, score: 62.675	N	N	N	N
vg0128647202	G -> DEL	LOC_Os01g49870.1	N	frameshift_variant	Average:30.663; most accessible tissue: Callus, score: 62.675	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0128647202	NA	7.25E-13	mr1612	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
vg0128647202	NA	1.99E-06	mr1652	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
vg0128647202	NA	1.55E-08	mr1989	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
vg0128647202	NA	9.92E-08	mr1126_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
vg0128647202	NA	5.44E-10	mr1166_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
vg0128647202	NA	1.81E-07	mr1567_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
vg0128647202	3.56E-06	NA	mr1593_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
vg0128647202	NA	6.87E-13	mr1612_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
vg0128647202	NA	1.62E-07	mr1765_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