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Detailed information for vg0903223470:

Variant ID: vg0903223470 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 3223470
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGACATGCCACCACGACATACCGGAAAGAGGCCGTGACAGGACCCTTCGCATAACCCCCTCTAGCCAAGCACACCACACCTCAGGTTTCACCCCCGTCCC[T/C]
AGCGAGCAACGGGCAGTCCCCTCTCGTGCCTAGGTGAATCCGGAAGCGACAGAGGCCGTCGCAGGGCCCGCCCCGCTCCATCACGCCCACCTTTGCCTGG

Reverse complement sequence

CCAGGCAAAGGTGGGCGTGATGGAGCGGGGCGGGCCCTGCGACGGCCTCTGTCGCTTCCGGATTCACCTAGGCACGAGAGGGGACTGCCCGTTGCTCGCT[A/G]
GGGACGGGGGTGAAACCTGAGGTGTGGTGTGCTTGGCTAGAGGGGGTTATGCGAAGGGTCCTGTCACGGCCTCTTTCCGGTATGTCGTGGTGGCATGTCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.70%	29.00%	14.39%	3.94%	NA
All Indica	2759	56.30%	13.50%	23.56%	6.63%	NA
All Japonica	1512	35.60%	64.20%	0.20%	0.00%	NA
Aus	269	92.90%	1.50%	4.46%	1.12%	NA
Indica I	595	51.90%	11.80%	30.25%	6.05%	NA
Indica II	465	44.30%	15.70%	26.45%	13.55%	NA
Indica III	913	67.50%	12.70%	17.31%	2.52%	NA
Indica Intermediate	786	53.80%	14.40%	24.05%	7.76%	NA
Temperate Japonica	767	2.50%	97.30%	0.26%	0.00%	NA
Tropical Japonica	504	79.60%	20.20%	0.20%	0.00%	NA
Japonica Intermediate	241	49.40%	50.60%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	57.80%	25.60%	16.67%	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
vg0903223470	T -> DEL	N	N	silent_mutation	Average:38.463; most accessible tissue: Zhenshan97 flag leaf, score: 76.356	N	N	N	N
vg0903223470	T -> C	LOC_Os09g06760.1	upstream_gene_variant ; 2253.0bp to feature; MODIFIER	silent_mutation	Average:38.463; most accessible tissue: Zhenshan97 flag leaf, score: 76.356	N	N	N	N
vg0903223470	T -> C	LOC_Os09g06750-LOC_Os09g06760	intergenic_region ; MODIFIER	silent_mutation	Average:38.463; most accessible tissue: Zhenshan97 flag leaf, score: 76.356	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0903223470	NA	1.08E-10	mr1084	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
vg0903223470	NA	3.28E-13	mr1205	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
vg0903223470	NA	8.08E-12	mr1206	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
vg0903223470	NA	1.76E-07	mr1206	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
vg0903223470	NA	4.38E-07	mr1220	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
vg0903223470	NA	4.98E-07	mr1229	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
vg0903223470	2.24E-06	6.45E-11	mr1596	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
vg0903223470	NA	8.45E-07	mr1596	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
vg0903223470	NA	5.43E-07	mr1880	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
vg0903223470	NA	6.79E-07	mr1042_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
vg0903223470	NA	7.75E-06	mr1206_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
vg0903223470	NA	2.76E-06	mr1359_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
vg0903223470	NA	5.62E-14	mr1593_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