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Detailed information for vg0421386227:

Variant ID: vg0421386227 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21386227
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGTTACTGTCTTGGTCCTCTTGGACATGAACTAAAATTTGATGTCAGAAATATTACTCCCTTCTTCCCTAAATGTTTGACGCCGTTGACTTTTTTAAA[C/T]
ATGTTTGACCGTTCGTCTTATTCAAAAACTTTTGTGAAATATGTAAAACTATATGTATACATAAAAGTATATTTAACAATGAATCAAATGGTAGGAAAAG

Reverse complement sequence

CTTTTCCTACCATTTGATTCATTGTTAAATATACTTTTATGTATACATATAGTTTTACATATTTCACAAAAGTTTTTGAATAAGACGAACGGTCAAACAT[G/A]
TTTAAAAAAGTCAACGGCGTCAAACATTTAGGGAAGAAGGGAGTAATATTTCTGACATCAAATTTTAGTTCATGTCCAAGAGGACCAAGACAGTAACAAA

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	78.20%	6.40%	0.83%	14.62%	NA
All Indica	2759	65.90%	8.70%	1.41%	24.07%	NA
All Japonica	1512	98.60%	1.30%	0.00%	0.07%	NA
Aus	269	94.10%	0.00%	0.00%	5.95%	NA
Indica I	595	67.60%	10.60%	1.18%	20.67%	NA
Indica II	465	74.40%	5.20%	1.72%	18.71%	NA
Indica III	913	57.90%	8.90%	1.64%	31.54%	NA
Indica Intermediate	786	68.70%	9.00%	1.15%	21.12%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	96.00%	3.80%	0.00%	0.20%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	57.30%	39.60%	0.00%	3.12%	NA
Intermediate	90	86.70%	5.60%	0.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0421386227	C -> DEL	N	N	silent_mutation	Average:67.087; most accessible tissue: Callus, score: 84.443	N	N	N	N
vg0421386227	C -> T	LOC_Os04g35190.1	downstream_gene_variant ; 875.0bp to feature; MODIFIER	silent_mutation	Average:67.087; most accessible tissue: Callus, score: 84.443	N	N	N	N
vg0421386227	C -> T	LOC_Os04g35200.1	intron_variant ; MODIFIER	silent_mutation	Average:67.087; most accessible tissue: Callus, score: 84.443	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421386227	4.45E-06	9.80E-08	mr1134_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
vg0421386227	1.46E-07	3.63E-10	mr1672_2	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