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Detailed information for vg0416229064:

Variant ID: vg0416229064 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 16229064
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTACAAATTATAACAACTTCAAACAACATTTTCAAATACTAAATGATTTCAACTGAAAAAGTCATCAACAACAAAGTTGTATAACTCATCAATATCTA[C/T]
AACTTTTTTTGGTCATTTCTTCATCCGATAAAGTTATAATAATATTGTACACAAAATTTATATATATATCTCTTATAGGTTATAAAACCATATAAGAGAT

Reverse complement sequence

ATCTCTTATATGGTTTTATAACCTATAAGAGATATATATATAAATTTTGTGTACAATATTATTATAACTTTATCGGATGAAGAAATGACCAAAAAAAGTT[G/A]
TAGATATTGATGAGTTATACAACTTTGTTGTTGATGACTTTTTCAGTTGAAATCATTTAGTATTTGAAAATGTTGTTTGAAGTTGTTATAATTTGTAATT

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	76.40%	1.10%	21.67%	0.80%	NA
All Indica	2759	83.60%	0.60%	15.01%	0.80%	NA
All Japonica	1512	64.40%	2.10%	32.61%	0.86%	NA
Aus	269	63.60%	1.10%	34.20%	1.12%	NA
Indica I	595	94.10%	0.20%	5.21%	0.50%	NA
Indica II	465	93.50%	0.40%	5.81%	0.22%	NA
Indica III	913	67.90%	0.80%	30.01%	1.31%	NA
Indica Intermediate	786	88.00%	0.80%	10.43%	0.76%	NA
Temperate Japonica	767	69.90%	1.20%	27.90%	1.04%	NA
Tropical Japonica	504	47.80%	3.80%	47.62%	0.79%	NA
Japonica Intermediate	241	81.70%	1.70%	16.18%	0.41%	NA
VI/Aromatic	96	84.40%	2.10%	13.54%	0.00%	NA
Intermediate	90	85.60%	1.10%	13.33%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0416229064	C -> DEL	N	N	silent_mutation	Average:35.242; most accessible tissue: Zhenshan97 young leaf, score: 50.669	N	N	N	N
vg0416229064	C -> T	LOC_Os04g27450.1	upstream_gene_variant ; 4654.0bp to feature; MODIFIER	silent_mutation	Average:35.242; most accessible tissue: Zhenshan97 young leaf, score: 50.669	N	N	N	N
vg0416229064	C -> T	LOC_Os04g27440.1	downstream_gene_variant ; 1312.0bp to feature; MODIFIER	silent_mutation	Average:35.242; most accessible tissue: Zhenshan97 young leaf, score: 50.669	N	N	N	N
vg0416229064	C -> T	LOC_Os04g27430-LOC_Os04g27440	intergenic_region ; MODIFIER	silent_mutation	Average:35.242; most accessible tissue: Zhenshan97 young leaf, score: 50.669	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0416229064	7.13E-07	7.13E-07	mr1440_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