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Detailed information for vg0619131736:

Variant ID: vg0619131736 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19131736
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.79, C: 0.22, others allele: 0.00, population size: 145. )

Flanking Sequence (100 bp) in Reference Genome:

TCGCGAGATACTGTTGTGAAATATTTACCGTGCCAACCACAAGCCAGCGTGGGCAACGGCTTTATCTTTTGTATAGCATGATTCATTATAGTGTGCCAGA[T/C]
TGTGAAGCGGCGAGAAGTCCGTGGGGGTCGCTGGGGAGTCCATTGCCTCTGGTTTTGAGGGGGAGATTATGATCCAGGAACGGTGCACTGTGGTGAGTTG

Reverse complement sequence

CAACTCACCACAGTGCACCGTTCCTGGATCATAATCTCCCCCTCAAAACCAGAGGCAATGGACTCCCCAGCGACCCCCACGGACTTCTCGCCGCTTCACA[A/G]
TCTGGCACACTATAATGAATCATGCTATACAAAAGATAAAGCCGTTGCCCACGCTGGCTTGTGGTTGGCACGGTAAATATTTCACAACAGTATCTCGCGA

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	95.50%	2.20%	1.90%	0.42%	NA
All Indica	2759	98.20%	0.10%	1.49%	0.18%	NA
All Japonica	1512	95.00%	2.00%	2.05%	0.99%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.60%	0.00%	2.35%	0.00%	NA
Indica II	465	99.40%	0.00%	0.65%	0.00%	NA
Indica III	913	99.30%	0.20%	0.22%	0.22%	NA
Indica Intermediate	786	96.60%	0.30%	2.80%	0.38%	NA
Temperate Japonica	767	96.30%	0.10%	2.87%	0.65%	NA
Tropical Japonica	504	94.00%	5.40%	0.20%	0.40%	NA
Japonica Intermediate	241	92.50%	0.80%	3.32%	3.32%	NA
VI/Aromatic	96	22.90%	60.40%	16.67%	0.00%	NA
Intermediate	90	85.60%	12.20%	2.22%	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
vg0619131736	T -> C	LOC_Os06g32880.1	upstream_gene_variant ; 3394.0bp to feature; MODIFIER	silent_mutation	Average:31.119; most accessible tissue: Zhenshan97 flag leaf, score: 51.466	N	N	N	N
vg0619131736	T -> C	LOC_Os06g32880-LOC_Os06g32890	intergenic_region ; MODIFIER	silent_mutation	Average:31.119; most accessible tissue: Zhenshan97 flag leaf, score: 51.466	N	N	N	N
vg0619131736	T -> DEL	N	N	silent_mutation	Average:31.119; most accessible tissue: Zhenshan97 flag leaf, score: 51.466	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619131736	4.42E-06	4.42E-06	mr1197	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