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Detailed information for vg0328074803:

Variant ID: vg0328074803 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 28074803
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGGTCGGTCGACCCAAATCCACAATAGTCCCGGTTCCATTAAAAACCGGGACTAAAAATGATTTTTAGTCCCGGTTAATAAGAGGAAGATCTTTAGTCC[C/T]
GGTTGGTAACTCCAACCGGGACTAAAGTTCATTTTTAGTCCCGGTTGATTCCATGTCAGGCCGTGTCAGGGCCCTAGGATCTTTAGTTCCGGTTAGTAAC

Reverse complement sequence

GTTACTAACCGGAACTAAAGATCCTAGGGCCCTGACACGGCCTGACATGGAATCAACCGGGACTAAAAATGAACTTTAGTCCCGGTTGGAGTTACCAACC[G/A]
GGACTAAAGATCTTCCTCTTATTAACCGGGACTAAAAATCATTTTTAGTCCCGGTTTTTAATGGAACCGGGACTATTGTGGATTTGGGTCGACCGACCAA

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	95.70%	3.80%	0.44%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	86.90%	11.80%	1.32%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	79.10%	18.40%	2.48%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	86.70%	12.90%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	1.11%	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
vg0328074803	C -> T	LOC_Os03g49330.1	upstream_gene_variant ; 1923.0bp to feature; MODIFIER	silent_mutation	Average:60.596; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0328074803	C -> T	LOC_Os03g49310-LOC_Os03g49330	intergenic_region ; MODIFIER	silent_mutation	Average:60.596; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0328074803	NA	7.21E-06	mr1050	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