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Detailed information for vg0327574120:

Variant ID: vg0327574120 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 27574120
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTCATCTATTTTCACCATGTATACACCCCTCAATACAAATTTAGGCACCCGTATCAGCTTAAATTTGATCTATAGTAGAGTAAATTAAGTAAGTGGCAC[C/T]
ACCCTCTGTTTCGCTCTAGCTCCGCCCCTATGCGTAAGGATGGGAATCATTGGGAATCAGTCGTTGCAGCATCTACCTCATCTCTCTCCCAGTTTCTCAT

Reverse complement sequence

ATGAGAAACTGGGAGAGAGATGAGGTAGATGCTGCAACGACTGATTCCCAATGATTCCCATCCTTACGCATAGGGGCGGAGCTAGAGCGAAACAGAGGGT[G/A]
GTGCCACTTACTTAATTTACTCTACTATAGATCAAATTTAAGCTGATACGGGTGCCTAAATTTGTATTGAGGGGTGTATACATGGTGAAAATAGATGAGG

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	95.20%	3.30%	1.50%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.11%	0.00%	NA
All Japonica	1512	85.30%	10.30%	4.50%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.00%	0.50%	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	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	76.00%	15.60%	8.34%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	84.20%	14.10%	1.66%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	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
vg0327574120	C -> T	LOC_Os03g48410-LOC_Os03g48430	intergenic_region ; MODIFIER	silent_mutation	Average:42.684; most accessible tissue: Zhenshan97 root, score: 58.674	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0327574120	3.20E-06	NA	mr1926	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
vg0327574120	1.41E-06	NA	mr1335_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
vg0327574120	2.42E-06	NA	mr1484_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
vg0327574120	1.34E-06	NA	mr1900_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