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Detailed information for vg0222211789:

Variant ID: vg0222211789 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22211789
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCATGCTCGCTCCGTACCTCTACCCCCCACTGCCGTGAGCCACCGCCGTCGTCCCCTTAGTCCTCCCATTACCGTGAGCCTCCGCGGCCGAGCCGCCG[C/T]
CCCTGGTTCTGCTGCGCCCCCATGCCGCCGACCGCTGCTGCCAACAAAGGAAGATAGAGTATAGGAGGGGAGTCGCTGACAGGTGGGTCCCACTTTATTT

Reverse complement sequence

AAATAAAGTGGGACCCACCTGTCAGCGACTCCCCTCCTATACTCTATCTTCCTTTGTTGGCAGCAGCGGTCGGCGGCATGGGGGCGCAGCAGAACCAGGG[G/A]
CGGCGGCTCGGCCGCGGAGGCTCACGGTAATGGGAGGACTAAGGGGACGACGGCGGTGGCTCACGGCAGTGGGGGGTAGAGGTACGGAGCGAGCATGGAC

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	34.90%	15.00%	1.14%	48.92%	NA
All Indica	2759	5.30%	24.90%	1.70%	68.07%	NA
All Japonica	1512	93.00%	0.70%	0.13%	6.22%	NA
Aus	269	0.00%	0.70%	0.37%	98.88%	NA
Indica I	595	4.50%	28.10%	1.34%	66.05%	NA
Indica II	465	1.50%	8.40%	3.01%	87.10%	NA
Indica III	913	3.90%	32.40%	0.33%	63.31%	NA
Indica Intermediate	786	9.70%	23.70%	2.80%	63.87%	NA
Temperate Japonica	767	98.30%	0.10%	0.13%	1.43%	NA
Tropical Japonica	504	83.50%	1.60%	0.20%	14.68%	NA
Japonica Intermediate	241	95.90%	0.40%	0.00%	3.73%	NA
VI/Aromatic	96	60.40%	1.00%	0.00%	38.54%	NA
Intermediate	90	44.40%	10.00%	4.44%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0222211789	C -> T	LOC_Os02g36830.1	upstream_gene_variant ; 3268.0bp to feature; MODIFIER	silent_mutation	Average:19.146; most accessible tissue: Callus, score: 94.658	N	N	N	N
vg0222211789	C -> T	LOC_Os02g36820.1	downstream_gene_variant ; 61.0bp to feature; MODIFIER	silent_mutation	Average:19.146; most accessible tissue: Callus, score: 94.658	N	N	N	N
vg0222211789	C -> T	LOC_Os02g36820-LOC_Os02g36830	intergenic_region ; MODIFIER	silent_mutation	Average:19.146; most accessible tissue: Callus, score: 94.658	N	N	N	N
vg0222211789	C -> DEL	N	N	silent_mutation	Average:19.146; most accessible tissue: Callus, score: 94.658	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222211789	8.50E-06	5.68E-06	mr1080	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
vg0222211789	2.47E-06	2.47E-06	mr1255	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
vg0222211789	2.77E-07	3.64E-09	mr1619	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