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Detailed information for vg0619238891:

Variant ID: vg0619238891 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19238891
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTATAAAACCTTTCCATTTATTTTATGTAATCTCTAACTTTGGCTCTAAATTATATTTCCTTTGAATCCATTCCCGAACACCTCCAACAAATACCCTTT[C/G]
AATTCCCGTTCAACCATCTCTAGAGCACATGAAATATCAATCTCTCTAGAGTTAATACCTTTTTATTTCGAGCTTACCACACTACCACCAAATCCAGTTT

Reverse complement sequence

AAACTGGATTTGGTGGTAGTGTGGTAAGCTCGAAATAAAAAGGTATTAACTCTAGAGAGATTGATATTTCATGTGCTCTAGAGATGGTTGAACGGGAATT[G/C]
AAAGGGTATTTGTTGGAGGTGTTCGGGAATGGATTCAAAGGAAATATAATTTAGAGCCAAAGTTAGAGATTACATAAAATAAATGGAAAGGTTTTATAAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.00%	0.10%	0.53%	4.32%	NA
All Indica	2759	99.80%	0.00%	0.00%	0.22%	NA
All Japonica	1512	85.10%	0.30%	1.59%	13.03%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.30%	0.00%	0.00%	0.67%	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	99.70%	0.00%	0.00%	0.25%	NA
Temperate Japonica	767	76.80%	0.50%	2.35%	20.34%	NA
Tropical Japonica	504	98.60%	0.20%	0.20%	0.99%	NA
Japonica Intermediate	241	83.00%	0.00%	2.07%	14.94%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	98.90%	0.00%	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
vg0619238891	C -> G	LOC_Os06g33040.1	upstream_gene_variant ; 4082.0bp to feature; MODIFIER	silent_mutation	Average:35.881; most accessible tissue: Minghui63 flag leaf, score: 51.386	N	N	N	N
vg0619238891	C -> G	LOC_Os06g33040-LOC_Os06g33050	intergenic_region ; MODIFIER	silent_mutation	Average:35.881; most accessible tissue: Minghui63 flag leaf, score: 51.386	N	N	N	N
vg0619238891	C -> DEL	N	N	silent_mutation	Average:35.881; most accessible tissue: Minghui63 flag leaf, score: 51.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619238891	1.36E-06	NA	mr1549	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
vg0619238891	NA	1.64E-09	mr1549	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
vg0619238891	NA	7.88E-08	mr1757	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
vg0619238891	NA	9.38E-06	mr1126_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
vg0619238891	NA	4.73E-07	mr1456_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
vg0619238891	NA	8.36E-06	mr1577_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
vg0619238891	NA	1.74E-07	mr1733_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
vg0619238891	NA	8.90E-06	mr1757_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
vg0619238891	NA	3.13E-06	mr1780_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