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Detailed information for vg0906300837:

Variant ID: vg0906300837 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6300837
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.66, G: 0.33, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

CCGCCTACGCGGCTGGCCTATTATGCCGCCGTTGTTGGGCATCCTCGTCTTCACCGACCGGCTTTCCTTCGTCGCCGCCGACTGGTGTTTCCGCCTGCAC[T/G]
GCTGGCCTATTATATGCTGCCGTTGTTGGGCGTCCGTCGACTGGTGTCCTCACCTATACGGTTGGCTGGTCACACCACCGTACATGGGCATCCACGTCTT

Reverse complement sequence

AAGACGTGGATGCCCATGTACGGTGGTGTGACCAGCCAACCGTATAGGTGAGGACACCAGTCGACGGACGCCCAACAACGGCAGCATATAATAGGCCAGC[A/C]
GTGCAGGCGGAAACACCAGTCGGCGGCGACGAAGGAAAGCCGGTCGGTGAAGACGAGGATGCCCAACAACGGCGGCATAATAGGCCAGCCGCGTAGGCGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.60%	18.80%	30.66%	7.89%	NA
All Indica	2759	16.20%	31.10%	44.94%	7.68%	NA
All Japonica	1512	98.10%	0.50%	1.32%	0.13%	NA
Aus	269	8.60%	0.70%	39.03%	51.67%	NA
Indica I	595	24.00%	10.40%	54.29%	11.26%	NA
Indica II	465	8.40%	55.50%	26.24%	9.89%	NA
Indica III	913	11.80%	29.90%	55.64%	2.63%	NA
Indica Intermediate	786	20.10%	33.80%	36.51%	9.54%	NA
Temperate Japonica	767	99.50%	0.30%	0.26%	0.00%	NA
Tropical Japonica	504	99.20%	0.40%	0.40%	0.00%	NA
Japonica Intermediate	241	91.30%	1.20%	6.64%	0.83%	NA
VI/Aromatic	96	11.50%	4.20%	67.71%	16.67%	NA
Intermediate	90	55.60%	18.90%	21.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906300837	T -> G	LOC_Os09g11350.1	upstream_gene_variant ; 84.0bp to feature; MODIFIER	silent_mutation	Average:48.501; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg0906300837	T -> G	LOC_Os09g11330.1	downstream_gene_variant ; 4885.0bp to feature; MODIFIER	silent_mutation	Average:48.501; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg0906300837	T -> G	LOC_Os09g11360.1	downstream_gene_variant ; 4771.0bp to feature; MODIFIER	silent_mutation	Average:48.501; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg0906300837	T -> G	LOC_Os09g11330-LOC_Os09g11350	intergenic_region ; MODIFIER	silent_mutation	Average:48.501; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg0906300837	T -> DEL	N	N	silent_mutation	Average:48.501; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906300837	1.11E-06	8.28E-06	mr1101	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
vg0906300837	NA	7.88E-06	mr1113	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
vg0906300837	9.57E-07	1.24E-07	mr1123	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
vg0906300837	NA	1.52E-06	mr1242	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
vg0906300837	NA	3.36E-06	mr1247	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
vg0906300837	3.50E-06	8.57E-07	mr1495	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
vg0906300837	5.52E-07	1.36E-07	mr1917	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
vg0906300837	NA	7.77E-06	mr1119_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
vg0906300837	NA	8.89E-06	mr1247_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