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Detailed information for vg0304745816:

Variant ID: vg0304745816 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 4745816
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCGTTGGCATATGGTGAACCTGTGTCGGCTTTCGAAATGCCTTGTCATGAAAGCCTTAAGGTCTCTAGTCGTGGCCGTTCTGCACGGGCTGGATGATC[C/T]
GGGTTAGTAATATCGTGTGGGTAAAGTGTACCCCCTCTGTAGAGGTTATTAAACTGTTCGAACAGCCGTGCCCACGGTCATGGGCGGATGTAAGGTGATT

Reverse complement sequence

AATCACCTTACATCCGCCCATGACCGTGGGCACGGCTGTTCGAACAGTTTAATAACCTCTACAGAGGGGGTACACTTTACCCACACGATATTACTAACCC[G/A]
GATCATCCAGCCCGTGCAGAACGGCCACGACTAGAGACCTTAAGGCTTTCATGACAAGGCATTTCGAAAGCCGACACAGGTTCACCATATGCCAACGAGA

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	91.50%	7.80%	0.72%	0.00%	NA
All Indica	2759	92.60%	6.70%	0.69%	0.00%	NA
All Japonica	1512	99.80%	0.10%	0.07%	0.00%	NA
Aus	269	43.90%	52.40%	3.72%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	85.60%	12.30%	2.15%	0.00%	NA
Indica III	913	91.90%	7.80%	0.33%	0.00%	NA
Indica Intermediate	786	91.90%	7.40%	0.76%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	62.50%	36.50%	1.04%	0.00%	NA
Intermediate	90	92.20%	4.40%	3.33%	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
vg0304745816	C -> T	LOC_Os03g09110.1	upstream_gene_variant ; 4504.0bp to feature; MODIFIER	silent_mutation	Average:33.334; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N
vg0304745816	C -> T	LOC_Os03g09120.1	downstream_gene_variant ; 2888.0bp to feature; MODIFIER	silent_mutation	Average:33.334; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N
vg0304745816	C -> T	LOC_Os03g09110-LOC_Os03g09120	intergenic_region ; MODIFIER	silent_mutation	Average:33.334; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0304745816	3.38E-08	NA	mr1090_2	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
vg0304745816	NA	1.04E-06	mr1567_2	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