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Detailed information for vg0220143787:

Variant ID: vg0220143787 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20143787
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

TTTCTGTAGTGGTGTGTTTTACAAAACCACAACTAAGAAGGTTTACAAAACCGTGCGGTTACCGCACAGTTATCACGGTTATCACGTGTGGTAATCTTTT[C/T]
AGTTTTTGAAACTATGGTATATCACATGGTAACCGTACGGTTTTCACGATAACCACGCGGTTAACATGGTAACTGCCAAACCATGGGGTGGCGATAACCA

Reverse complement sequence

TGGTTATCGCCACCCCATGGTTTGGCAGTTACCATGTTAACCGCGTGGTTATCGTGAAAACCGTACGGTTACCATGTGATATACCATAGTTTCAAAAACT[G/A]
AAAAGATTACCACACGTGATAACCGTGATAACTGTGCGGTAACCGCACGGTTTTGTAAACCTTCTTAGTTGTGGTTTTGTAAAACACACCACTACAGAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.20%	39.10%	1.84%	5.90%	NA
All Indica	2759	78.80%	8.60%	2.83%	9.79%	NA
All Japonica	1512	8.50%	91.20%	0.20%	0.13%	NA
Aus	269	65.40%	32.30%	1.12%	1.12%	NA
Indica I	595	72.90%	14.80%	4.54%	7.73%	NA
Indica II	465	75.90%	12.70%	2.15%	9.25%	NA
Indica III	913	82.10%	3.40%	1.64%	12.81%	NA
Indica Intermediate	786	80.90%	7.60%	3.31%	8.14%	NA
Temperate Japonica	767	9.50%	90.40%	0.13%	0.00%	NA
Tropical Japonica	504	6.50%	93.30%	0.00%	0.20%	NA
Japonica Intermediate	241	9.10%	89.60%	0.83%	0.41%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	34.40%	57.80%	3.33%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0220143787	C -> T	LOC_Os02g33750.1	upstream_gene_variant ; 3059.0bp to feature; MODIFIER	silent_mutation	Average:57.466; most accessible tissue: Callus, score: 90.81	N	N	N	N
vg0220143787	C -> T	LOC_Os02g33770.1	upstream_gene_variant ; 4079.0bp to feature; MODIFIER	silent_mutation	Average:57.466; most accessible tissue: Callus, score: 90.81	N	N	N	N
vg0220143787	C -> T	LOC_Os02g33750.2	upstream_gene_variant ; 3059.0bp to feature; MODIFIER	silent_mutation	Average:57.466; most accessible tissue: Callus, score: 90.81	N	N	N	N
vg0220143787	C -> T	LOC_Os02g33750-LOC_Os02g33770	intergenic_region ; MODIFIER	silent_mutation	Average:57.466; most accessible tissue: Callus, score: 90.81	N	N	N	N
vg0220143787	C -> DEL	N	N	silent_mutation	Average:57.466; most accessible tissue: Callus, score: 90.81	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220143787	NA	5.68E-06	mr1103	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
vg0220143787	NA	8.04E-06	mr1107	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
vg0220143787	NA	7.29E-08	mr1162	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
vg0220143787	NA	4.68E-10	mr1379	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
vg0220143787	NA	6.96E-19	mr1518	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
vg0220143787	NA	7.25E-13	mr1630	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
vg0220143787	NA	1.55E-07	mr1804	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
vg0220143787	NA	1.81E-06	mr1691_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