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Detailed information for vg0919230422:

Variant ID: vg0919230422 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 19230422
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

TTGCGATGACAGGACGGCGCACTGCCACCGTAGGACGACCAACCACCAAGCCTTTGCCGCTAGCTCCACCCTTCTCTCTCTCCTCTCCCCCCTGCGATGA[C/A]
AGGACGGCGCACTGCCACCCTAGGATGACCAACCACCAAGCCTTCACCGCTAGTTCCATCCTTCTCTCTCTCCCTCCTCTCCCATGTGTTGCGTGCGTGC

Reverse complement sequence

GCACGCACGCAACACATGGGAGAGGAGGGAGAGAGAGAAGGATGGAACTAGCGGTGAAGGCTTGGTGGTTGGTCATCCTAGGGTGGCAGTGCGCCGTCCT[G/T]
TCATCGCAGGGGGGAGAGGAGAGAGAGAAGGGTGGAGCTAGCGGCAAAGGCTTGGTGGTTGGTCGTCCTACGGTGGCAGTGCGCCGTCCTGTCATCGCAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.70%	8.30%	0.00%	0.00%	NA
All Indica	2759	85.80%	14.20%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	89.70%	10.30%	0.00%	0.00%	NA
Indica III	913	77.30%	22.70%	0.00%	0.00%	NA
Indica Intermediate	786	82.70%	17.30%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	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
vg0919230422	C -> A	LOC_Os09g32210.1	upstream_gene_variant ; 2858.0bp to feature; MODIFIER	silent_mutation	Average:63.524; most accessible tissue: Zhenshan97 young leaf, score: 81.353	N	N	N	N
vg0919230422	C -> A	LOC_Os09g32220.1	upstream_gene_variant ; 4771.0bp to feature; MODIFIER	silent_mutation	Average:63.524; most accessible tissue: Zhenshan97 young leaf, score: 81.353	N	N	N	N
vg0919230422	C -> A	LOC_Os09g32210-LOC_Os09g32220	intergenic_region ; MODIFIER	silent_mutation	Average:63.524; most accessible tissue: Zhenshan97 young leaf, score: 81.353	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0919230422	1.65E-06	NA	mr1598	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