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Detailed information for vg0911270881:

Variant ID: vg0911270881 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11270881
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAGATAGGAAGTGACATGATTAACCGTTCGATCGTCCGACCCATCCAACCTTCGTTTCCTAGAGAGAGAAGTTTCTTTGAGAACTTGTACTTGGTGATT[A/G]
CAATTTTATTTCAAACTTTGGAAATTTCAGAACCCCAGCAAGTCATCATCTCAATCGAAATGTTTGGGTTTTTTCAATTTTTTGTTGAATTTAGTCAAAG

Reverse complement sequence

CTTTGACTAAATTCAACAAAAAATTGAAAAAACCCAAACATTTCGATTGAGATGATGACTTGCTGGGGTTCTGAAATTTCCAAAGTTTGAAATAAAATTG[T/C]
AATCACCAAGTACAAGTTCTCAAAGAAACTTCTCTCTCTAGGAAACGAAGGTTGGATGGGTCGGACGATCGAACGGTTAATCATGTCACTTCCTATCTTT

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	62.80%	31.40%	0.93%	4.82%	NA
All Indica	2759	95.90%	1.20%	0.22%	2.72%	NA
All Japonica	1512	12.20%	87.60%	0.13%	0.07%	NA
Aus	269	30.50%	1.50%	13.01%	55.02%	NA
Indica I	595	96.50%	1.00%	0.00%	2.52%	NA
Indica II	465	92.30%	1.70%	0.65%	5.38%	NA
Indica III	913	98.10%	0.30%	0.00%	1.53%	NA
Indica Intermediate	786	95.00%	1.90%	0.38%	2.67%	NA
Temperate Japonica	767	8.90%	90.90%	0.26%	0.00%	NA
Tropical Japonica	504	17.50%	82.50%	0.00%	0.00%	NA
Japonica Intermediate	241	12.00%	87.60%	0.00%	0.41%	NA
VI/Aromatic	96	15.60%	80.20%	1.04%	3.12%	NA
Intermediate	90	44.40%	54.40%	0.00%	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
vg0911270881	A -> G	LOC_Os09g18360.1	upstream_gene_variant ; 2838.0bp to feature; MODIFIER	silent_mutation	Average:33.062; most accessible tissue: Callus, score: 49.257	N	N	N	N
vg0911270881	A -> G	LOC_Os09g18370.1	downstream_gene_variant ; 4006.0bp to feature; MODIFIER	silent_mutation	Average:33.062; most accessible tissue: Callus, score: 49.257	N	N	N	N
vg0911270881	A -> G	LOC_Os09g18360-LOC_Os09g18370	intergenic_region ; MODIFIER	silent_mutation	Average:33.062; most accessible tissue: Callus, score: 49.257	N	N	N	N
vg0911270881	A -> DEL	N	N	silent_mutation	Average:33.062; most accessible tissue: Callus, score: 49.257	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911270881	6.36E-08	6.36E-08	mr1470	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
vg0911270881	NA	9.85E-07	mr1321_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
vg0911270881	NA	6.34E-16	mr1842_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