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Detailed information for vg0222517140:

Variant ID: vg0222517140 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22517140
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTTTTTTTGATTTTTTTTATTTGTGGTTTGGATGTTTTTATCTGTGATTGAATGTATGAATCTGTGATGTGGTGACTGAGTATGTGACTCGATGTTGT[T/C]
AATGAACCTGTGAATCAATATTGTGAATATATTTGTGATGTTGTGAACGAATATGTGAATGAATTTGTGATGAATCTGTGAATTGTGCTGTGGAGTTGTG

Reverse complement sequence

CACAACTCCACAGCACAATTCACAGATTCATCACAAATTCATTCACATATTCGTTCACAACATCACAAATATATTCACAATATTGATTCACAGGTTCATT[A/G]
ACAACATCGAGTCACATACTCAGTCACCACATCACAGATTCATACATTCAATCACAGATAAAAACATCCAAACCACAAATAAAAAAAATCAAAAAAAAAG

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	38.90%	1.20%	8.68%	51.25%	NA
All Indica	2759	8.40%	1.80%	11.53%	78.25%	NA
All Japonica	1512	95.60%	0.30%	0.79%	3.31%	NA
Aus	269	3.30%	0.40%	27.51%	68.77%	NA
Indica I	595	17.80%	1.30%	4.20%	76.64%	NA
Indica II	465	1.90%	1.10%	8.17%	88.82%	NA
Indica III	913	2.70%	2.40%	19.61%	75.25%	NA
Indica Intermediate	786	11.60%	2.00%	9.67%	76.72%	NA
Temperate Japonica	767	97.80%	0.50%	1.04%	0.65%	NA
Tropical Japonica	504	91.10%	0.00%	0.40%	8.53%	NA
Japonica Intermediate	241	98.30%	0.00%	0.83%	0.83%	NA
VI/Aromatic	96	94.80%	0.00%	2.08%	3.12%	NA
Intermediate	90	66.70%	1.10%	4.44%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0222517140	T -> DEL	N	N	silent_mutation	Average:23.888; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N
vg0222517140	T -> C	LOC_Os02g37254.1	upstream_gene_variant ; 1625.0bp to feature; MODIFIER	silent_mutation	Average:23.888; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N
vg0222517140	T -> C	LOC_Os02g37254-LOC_Os02g37260	intergenic_region ; MODIFIER	silent_mutation	Average:23.888; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222517140	6.69E-06	NA	mr1101	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
vg0222517140	4.69E-06	NA	mr1101	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