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Detailed information for vg0909319739:

Variant ID: vg0909319739 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9319739
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTATACACTACTACAGAAAGGGTAATAGGTGTCGGTTCAGAAACGCTAATAGGTGCCGGTTTTCCGAACCAGCACAAAGGAGGCTGCACTGATGATACT[G/T]
GTAATAAGATGCGGAGGTGCCGGTTCTAAGCCAAAGAGCCCTGTGGCTGTCAAATAGGTGCCGGTTTTTAGGTTAAAACCGGCACCTATATGGTCCTAAT

Reverse complement sequence

ATTAGGACCATATAGGTGCCGGTTTTAACCTAAAAACCGGCACCTATTTGACAGCCACAGGGCTCTTTGGCTTAGAACCGGCACCTCCGCATCTTATTAC[C/A]
AGTATCATCAGTGCAGCCTCCTTTGTGCTGGTTCGGAAAACCGGCACCTATTAGCGTTTCTGAACCGACACCTATTACCCTTTCTGTAGTAGTGTATAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.10%	3.70%	16.50%	43.76%	NA
All Indica	2759	15.10%	4.00%	20.44%	60.49%	NA
All Japonica	1512	80.10%	1.90%	2.51%	15.54%	NA
Aus	269	4.80%	7.80%	46.10%	41.26%	NA
Indica I	595	13.60%	3.90%	27.23%	55.29%	NA
Indica II	465	6.00%	3.00%	17.63%	73.33%	NA
Indica III	913	24.10%	4.50%	17.20%	54.22%	NA
Indica Intermediate	786	11.10%	4.10%	20.74%	64.12%	NA
Temperate Japonica	767	88.30%	0.50%	0.91%	10.30%	NA
Tropical Japonica	504	77.20%	3.20%	4.37%	15.28%	NA
Japonica Intermediate	241	60.20%	3.30%	3.73%	32.78%	NA
VI/Aromatic	96	18.80%	10.40%	42.71%	28.12%	NA
Intermediate	90	52.20%	4.40%	14.44%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909319739	G -> DEL	N	N	silent_mutation	Average:45.899; most accessible tissue: Zhenshan97 young leaf, score: 77.736	N	N	N	N
vg0909319739	G -> T	LOC_Os09g15280.1	upstream_gene_variant ; 3084.0bp to feature; MODIFIER	silent_mutation	Average:45.899; most accessible tissue: Zhenshan97 young leaf, score: 77.736	N	N	N	N
vg0909319739	G -> T	LOC_Os09g15270.1	downstream_gene_variant ; 4888.0bp to feature; MODIFIER	silent_mutation	Average:45.899; most accessible tissue: Zhenshan97 young leaf, score: 77.736	N	N	N	N
vg0909319739	G -> T	LOC_Os09g15284.1	downstream_gene_variant ; 244.0bp to feature; MODIFIER	silent_mutation	Average:45.899; most accessible tissue: Zhenshan97 young leaf, score: 77.736	N	N	N	N
vg0909319739	G -> T	LOC_Os09g15290.1	downstream_gene_variant ; 2923.0bp to feature; MODIFIER	silent_mutation	Average:45.899; most accessible tissue: Zhenshan97 young leaf, score: 77.736	N	N	N	N
vg0909319739	G -> T	LOC_Os09g15280-LOC_Os09g15284	intergenic_region ; MODIFIER	silent_mutation	Average:45.899; most accessible tissue: Zhenshan97 young leaf, score: 77.736	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909319739	3.36E-06	3.36E-06	mr1177_2	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
vg0909319739	NA	7.16E-07	mr1702_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