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Detailed information for vg0619482001:

Variant ID: vg0619482001 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19482001
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCACACGAATTGTGGTCAATCTAGCAACAGGTGAGTAAGTGTCAATCACACCACCAGAACAAACTGAACATACACATGAACTTGTCTCTGAGGAGGATG[T/C]
CAGTGAAGCAGCAGAAACAGCAGATCAATTTGGTGTGGATGATGTGCTAGGCACTGTGATTTTAATTCCAACAGAAGCATGAACAGAAGCATCGGCAAAA

Reverse complement sequence

TTTTGCCGATGCTTCTGTTCATGCTTCTGTTGGAATTAAAATCACAGTGCCTAGCACATCATCCACACCAAATTGATCTGCTGTTTCTGCTGCTTCACTG[A/G]
CATCCTCCTCAGAGACAAGTTCATGTGTATGTTCAGTTTGTTCTGGTGGTGTGATTGACACTTACTCACCTGTTGCTAGATTGACCACAATTCGTGTGCT

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	31.50%	1.90%	17.35%	49.22%	NA
All Indica	2759	3.40%	0.70%	22.22%	73.69%	NA
All Japonica	1512	89.40%	4.40%	1.85%	4.43%	NA
Aus	269	3.70%	0.00%	56.51%	39.78%	NA
Indica I	595	4.50%	0.20%	14.45%	80.84%	NA
Indica II	465	3.70%	1.10%	13.33%	81.94%	NA
Indica III	913	2.00%	0.00%	32.31%	65.72%	NA
Indica Intermediate	786	4.10%	1.70%	21.63%	72.65%	NA
Temperate Japonica	767	96.60%	0.10%	0.26%	3.00%	NA
Tropical Japonica	504	76.80%	11.30%	4.56%	7.34%	NA
Japonica Intermediate	241	92.50%	3.30%	1.24%	2.90%	NA
VI/Aromatic	96	2.10%	0.00%	12.50%	85.42%	NA
Intermediate	90	35.60%	6.70%	16.67%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0619482001	T -> C	LOC_Os06g33440.1	upstream_gene_variant ; 141.0bp to feature; MODIFIER	silent_mutation	Average:15.423; most accessible tissue: Callus, score: 48.319	N	N	N	N
vg0619482001	T -> C	LOC_Os06g33440-LOC_Os06g33450	intergenic_region ; MODIFIER	silent_mutation	Average:15.423; most accessible tissue: Callus, score: 48.319	N	N	N	N
vg0619482001	T -> DEL	N	N	silent_mutation	Average:15.423; most accessible tissue: Callus, score: 48.319	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619482001	NA	1.74E-07	mr1188_2	Jap_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
vg0619482001	NA	3.82E-06	mr1217_2	Jap_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
vg0619482001	2.95E-06	1.49E-09	mr1218_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
vg0619482001	NA	1.69E-08	mr1850_2	Jap_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