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Detailed information for vg0903570719:

Variant ID: vg0903570719 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 3570719
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGCCGCAGAAGCCTTTTCCTCAACATGATGCGGTGACGGCAGGCGTACGGCGCGGAGATGGCAGCGACAGCCATCCATACCCCTTCCGTCTCCTCGTCG[A/G]
CGGGGGTATGGCGCGAAGACAGTGACGACGGCCGTCCCTCCCCTCTCTCCCTCTCCTCCTTAGCCTCTTCGTTTCTGCCATCAAATCAGGGAGACGGTGG

Reverse complement sequence

CCACCGTCTCCCTGATTTGATGGCAGAAACGAAGAGGCTAAGGAGGAGAGGGAGAGAGGGGAGGGACGGCCGTCGTCACTGTCTTCGCGCCATACCCCCG[T/C]
CGACGAGGAGACGGAAGGGGTATGGATGGCTGTCGCTGCCATCTCCGCGCCGTACGCCTGCCGTCACCGCATCATGTTGAGGAAAAGGCTTCTGCGGCCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.60%	11.60%	1.06%	2.81%	NA
All Indica	2759	99.60%	0.20%	0.18%	0.04%	NA
All Japonica	1512	53.20%	35.30%	2.91%	8.66%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.20%	0.50%	0.34%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	99.90%	0.00%	0.00%	0.11%	NA
Indica Intermediate	786	99.50%	0.30%	0.25%	0.00%	NA
Temperate Japonica	767	30.00%	63.90%	4.04%	2.09%	NA
Tropical Japonica	504	82.10%	0.80%	0.60%	16.47%	NA
Japonica Intermediate	241	66.40%	16.20%	4.15%	13.28%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	10.00%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0903570719	A -> G	LOC_Os09g07270-LOC_Os09g07280	intergenic_region ; MODIFIER	silent_mutation	Average:81.571; most accessible tissue: Zhenshan97 young leaf, score: 90.456	N	N	N	N
vg0903570719	A -> DEL	N	N	silent_mutation	Average:81.571; most accessible tissue: Zhenshan97 young leaf, score: 90.456	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0903570719	3.31E-06	3.30E-06	mr1601	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