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Detailed information for vg0218685673:

Variant ID: vg0218685673 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 18685673
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, T: 0.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

ACAAAGAAACCATATTCCGAGACCAAGCTATCTCCAACTTGACTCATTAGTAGCAAACAGTAGTATTACATACGTATAGTATCCATCTAGAAGTCATAAT[C/T]
ATGAAATAATCACGGATATCCAAACAAACAACCCGAAACCGAAACTGACACAGCGTCGGCCGGTCAGACCGCGGGCTGCGCCGGTCTGACCGCGCATTAC

Reverse complement sequence

GTAATGCGCGGTCAGACCGGCGCAGCCCGCGGTCTGACCGGCCGACGCTGTGTCAGTTTCGGTTTCGGGTTGTTTGTTTGGATATCCGTGATTATTTCAT[G/A]
ATTATGACTTCTAGATGGATACTATACGTATGTAATACTACTGTTTGCTACTAATGAGTCAAGTTGGAGATAGCTTGGTCTCGGAATATGGTTTCTTTGT

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	89.10%	5.80%	3.30%	1.80%	NA
All Indica	2759	91.20%	3.30%	3.62%	1.88%	NA
All Japonica	1512	83.50%	11.20%	3.37%	1.92%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	90.80%	2.80%	4.09%	2.37%	NA
Indica III	913	81.20%	7.20%	7.45%	4.16%	NA
Indica Intermediate	786	96.30%	1.70%	1.65%	0.38%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	67.50%	21.60%	6.55%	4.37%	NA
Japonica Intermediate	241	67.60%	22.00%	7.47%	2.90%	NA
VI/Aromatic	96	86.50%	9.40%	3.12%	1.04%	NA
Intermediate	90	91.10%	3.30%	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
vg0218685673	C -> T	LOC_Os02g31190.1	upstream_gene_variant ; 1429.0bp to feature; MODIFIER	silent_mutation	Average:57.593; most accessible tissue: Minghui63 root, score: 77.009	N	N	N	N
vg0218685673	C -> T	LOC_Os02g31190-LOC_Os02g31200	intergenic_region ; MODIFIER	silent_mutation	Average:57.593; most accessible tissue: Minghui63 root, score: 77.009	N	N	N	N
vg0218685673	C -> DEL	N	N	silent_mutation	Average:57.593; most accessible tissue: Minghui63 root, score: 77.009	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0218685673	8.89E-06	4.12E-07	mr1050	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
vg0218685673	NA	2.47E-09	mr1093	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
vg0218685673	5.02E-08	4.66E-10	mr1272	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
vg0218685673	NA	2.62E-06	mr1408	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
vg0218685673	NA	5.54E-08	mr1089_2	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
vg0218685673	NA	2.12E-10	mr1093_2	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
vg0218685673	NA	3.17E-06	mr1113_2	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
vg0218685673	NA	3.41E-06	mr1114_2	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
vg0218685673	NA	1.99E-06	mr1138_2	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
vg0218685673	NA	1.48E-12	mr1178_2	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
vg0218685673	NA	3.44E-08	mr1235_2	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
vg0218685673	NA	8.30E-06	mr1258_2	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
vg0218685673	NA	1.20E-06	mr1552_2	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
vg0218685673	NA	5.41E-08	mr1599_2	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