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Detailed information for vg0221004561:

Variant ID: vg0221004561 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21004561
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 128. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCTTTACGAGTATGGAGAGAGTATTCAGTTAGATGACTACTAAATGCTTTCTGTGGTCTCAGTGAGGTTTTAATGATGCTTCTACACAACCAAACAAG[C/T]
AAAACCCCGGGAAGAACGAAAATATAACTGCATACATGTTTAGCCATGCCAAAGTCCGCAAGTTTGACTTCACCATTAGGGCCCACAAGTATGTTTGCTC

Reverse complement sequence

GAGCAAACATACTTGTGGGCCCTAATGGTGAAGTCAAACTTGCGGACTTTGGCATGGCTAAACATGTATGCAGTTATATTTTCGTTCTTCCCGGGGTTTT[G/A]
CTTGTTTGGTTGTGTAGAAGCATCATTAAAACCTCACTGAGACCACAGAAAGCATTTAGTAGTCATCTAACTGAATACTCTCTCCATACTCGTAAAGGAA

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	56.90%	42.60%	0.23%	0.30%	NA
All Indica	2759	38.20%	61.00%	0.33%	0.47%	NA
All Japonica	1512	94.00%	5.90%	0.07%	0.00%	NA
Aus	269	21.20%	78.40%	0.37%	0.00%	NA
Indica I	595	21.50%	78.00%	0.17%	0.34%	NA
Indica II	465	35.10%	64.30%	0.22%	0.43%	NA
Indica III	913	56.80%	42.30%	0.33%	0.55%	NA
Indica Intermediate	786	31.20%	67.80%	0.51%	0.51%	NA
Temperate Japonica	767	93.40%	6.60%	0.00%	0.00%	NA
Tropical Japonica	504	95.00%	5.00%	0.00%	0.00%	NA
Japonica Intermediate	241	94.20%	5.40%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	66.70%	32.20%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0221004561	C -> T	LOC_Os02g35010.1	intron_variant ; MODIFIER	silent_mutation	Average:55.167; most accessible tissue: Minghui63 flag leaf, score: 72.028	N	N	N	N
vg0221004561	C -> DEL	N	N	silent_mutation	Average:55.167; most accessible tissue: Minghui63 flag leaf, score: 72.028	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221004561	2.12E-06	3.68E-06	mr1101	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
vg0221004561	NA	1.63E-07	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
vg0221004561	NA	6.42E-13	mr1441	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
vg0221004561	NA	1.25E-06	mr1510	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
vg0221004561	6.20E-07	1.03E-06	mr1911	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
vg0221004561	NA	4.74E-06	mr1961	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
vg0221004561	1.43E-06	7.82E-08	mr1098_2	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
vg0221004561	NA	1.59E-06	mr1150_2	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