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Detailed information for vg0416113157:

Variant ID: vg0416113157 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 16113157
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTAAACAGAATCTCGTTCTCGAGATTCGGAAGAGCTGGCGAAAAGATGCTTATGAGCTGACTTTAATTCATCTTCTCGTTTCCAAGTAGCTTCTTCTTC[T/C]
GAGTGATTACTCCATTGGACCTTGCAAAAACGGATAACTCGATTCCTGGTTCTTCTCTCATCTGTCTCCAGGATACGGATTGGTTTCTCAACATATGTCA

Reverse complement sequence

TGACATATGTTGAGAAACCAATCCGTATCCTGGAGACAGATGAGAGAAGAACCAGGAATCGAGTTATCCGTTTTTGCAAGGTCCAATGGAGTAATCACTC[A/G]
GAAGAAGAAGCTACTTGGAAACGAGAAGATGAATTAAAGTCAGCTCATAAGCATCTTTTCGCCAGCTCTTCCGAATCTCGAGAACGAGATTCTGTTTAAG

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	85.20%	5.80%	3.00%	6.01%	NA
All Indica	2759	83.50%	9.60%	3.15%	3.77%	NA
All Japonica	1512	99.70%	0.00%	0.13%	0.20%	NA
Aus	269	33.80%	0.00%	14.87%	51.30%	NA
Indica I	595	95.80%	0.20%	2.02%	2.02%	NA
Indica II	465	89.90%	3.20%	3.01%	3.87%	NA
Indica III	913	69.70%	21.20%	4.05%	5.04%	NA
Indica Intermediate	786	86.40%	7.00%	3.05%	3.56%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.40%	0.20%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	51.00%	4.20%	11.46%	33.33%	NA
Intermediate	90	85.60%	4.40%	2.22%	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
vg0416113157	T -> C	LOC_Os04g27270.1	downstream_gene_variant ; 120.0bp to feature; MODIFIER	silent_mutation	Average:31.727; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0416113157	T -> C	LOC_Os04g27260-LOC_Os04g27270	intergenic_region ; MODIFIER	silent_mutation	Average:31.727; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0416113157	T -> DEL	N	N	silent_mutation	Average:31.727; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0416113157	1.48E-06	1.48E-06	mr1391_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