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Detailed information for vg0220287168:

Variant ID: vg0220287168 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20287168
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 54. )

Flanking Sequence (100 bp) in Reference Genome:

CCATGTACCAACTTACCAAGTGGTAGTGAGGAGGTATCACTGGTGGAGAAACCCTTTGTAGTCCCGGTTCGTAACCCCCCTTTAGTCCCGGTTTCCAAAC[T/C]
GGGAGTACCAATCCGGGACTAAAGATCGCTATCTTTAGTCCCGGATGAAATAACCGGGACTAAAGATAGATCTGACCTTTTTTTTTGCATGGCCCTGTTG

Reverse complement sequence

CAACAGGGCCATGCAAAAAAAAAGGTCAGATCTATCTTTAGTCCCGGTTATTTCATCCGGGACTAAAGATAGCGATCTTTAGTCCCGGATTGGTACTCCC[A/G]
GTTTGGAAACCGGGACTAAAGGGGGGTTACGAACCGGGACTACAAAGGGTTTCTCCACCAGTGATACCTCCTCACTACCACTTGGTAAGTTGGTACATGG

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	19.80%	19.70%	0.72%	59.78%	NA
All Indica	2759	6.70%	1.20%	1.01%	91.05%	NA
All Japonica	1512	48.00%	50.20%	0.13%	1.65%	NA
Aus	269	0.00%	5.90%	0.00%	94.05%	NA
Indica I	595	12.90%	0.50%	0.00%	86.55%	NA
Indica II	465	9.20%	1.10%	0.65%	89.03%	NA
Indica III	913	2.50%	1.40%	2.30%	93.76%	NA
Indica Intermediate	786	5.30%	1.70%	0.51%	92.49%	NA
Temperate Japonica	767	53.20%	45.50%	0.26%	1.04%	NA
Tropical Japonica	504	45.80%	52.80%	0.00%	1.39%	NA
Japonica Intermediate	241	36.10%	59.80%	0.00%	4.15%	NA
VI/Aromatic	96	0.00%	94.80%	0.00%	5.21%	NA
Intermediate	90	25.60%	36.70%	4.44%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0220287168	T -> DEL	N	N	silent_mutation	Average:26.383; most accessible tissue: Zhenshan97 young leaf, score: 40.52	N	N	N	N
vg0220287168	T -> C	LOC_Os02g33990.1	downstream_gene_variant ; 383.0bp to feature; MODIFIER	silent_mutation	Average:26.383; most accessible tissue: Zhenshan97 young leaf, score: 40.52	N	N	N	N
vg0220287168	T -> C	LOC_Os02g33980-LOC_Os02g33990	intergenic_region ; MODIFIER	silent_mutation	Average:26.383; most accessible tissue: Zhenshan97 young leaf, score: 40.52	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220287168	1.68E-06	1.68E-06	mr1655_2	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
vg0220287168	1.19E-07	1.19E-07	mr1657_2	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
vg0220287168	4.87E-06	4.87E-06	mr1669_2	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