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Detailed information for vg0200448299:

Variant ID: vg0200448299 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 448299
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGGGGGTGGGGGGTGGGGAGTGAAGGAATATTTACAGATACTTTTGTGGGTACAAACGGACGATTTTCCTACCATGTTTTTTCGAGGTTTCTTAATTGT[C/T]
AACTTTAAAAATAGTATCAAGACATGGTACTATTTATAACATAGGAAAAGTTCTATAATTAATATTTAGACAAATAAGTTCGATACATCTTACTCCCTCC

Reverse complement sequence

GGAGGGAGTAAGATGTATCGAACTTATTTGTCTAAATATTAATTATAGAACTTTTCCTATGTTATAAATAGTACCATGTCTTGATACTATTTTTAAAGTT[G/A]
ACAATTAAGAAACCTCGAAAAAACATGGTAGGAAAATCGTCCGTTTGTACCCACAAAAGTATCTGTAAATATTCCTTCACTCCCCACCCCCCACCCCCCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.00%	5.00%	0.04%	0.00%	NA
All Indica	2759	93.90%	6.00%	0.07%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	93.70%	6.30%	0.00%	0.00%	NA
Indica I	595	92.90%	6.90%	0.17%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	93.10%	6.80%	0.11%	0.00%	NA
Indica Intermediate	786	93.40%	6.60%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	57.30%	42.70%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0200448299	C -> T	LOC_Os02g01800.1	downstream_gene_variant ; 2299.0bp to feature; MODIFIER	silent_mutation	Average:53.998; most accessible tissue: Callus, score: 94.109	N	N	N	N
vg0200448299	C -> T	LOC_Os02g01820.1	downstream_gene_variant ; 3172.0bp to feature; MODIFIER	silent_mutation	Average:53.998; most accessible tissue: Callus, score: 94.109	N	N	N	N
vg0200448299	C -> T	LOC_Os02g01810.1	intron_variant ; MODIFIER	silent_mutation	Average:53.998; most accessible tissue: Callus, score: 94.109	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0200448299	7.16E-07	NA	mr1458_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
vg0200448299	NA	4.75E-06	mr1875_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
vg0200448299	NA	3.78E-06	mr1908_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