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Detailed information for vg0910357999:

Variant ID: vg0910357999 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10357999
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAAGATGTTTCAGGATGCGGCAGTCTTTAGCGACATGAGTGTCAGATCCACACCTGTTGCAATGCTTGTTGCCATTACTACGAGGTTGTGGTGCCTTAC[T/C]
CTTCCCTTTTCCTTTCTTTCGACCCTTGAATTTGCGCCTGTTGTTGTTGCGTTTGCGCTTTCCAGTCAGATTCTTAGGATTATTCGAAGAATTTCCCTTG

Reverse complement sequence

CAAGGGAAATTCTTCGAATAATCCTAAGAATCTGACTGGAAAGCGCAAACGCAACAACAACAGGCGCAAATTCAAGGGTCGAAAGAAAGGAAAAGGGAAG[A/G]
GTAAGGCACCACAACCTCGTAGTAATGGCAACAAGCATTGCAACAGGTGTGGATCTGACACTCATGTCGCTAAAGACTGCCGCATCCTGAAACATCTTGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.60%	0.20%	0.19%	0.00%	NA
All Indica	2759	99.30%	0.30%	0.33%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.70%	0.80%	0.50%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	99.30%	0.40%	0.22%	0.00%	NA
Indica Intermediate	786	99.70%	0.00%	0.25%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0910357999	T -> C	LOC_Os09g16940.1	missense_variant ; p.Ser365Gly; MODERATE	N	Average:11.889; most accessible tissue: Zhenshan97 flag leaf, score: 17.069	N	N	N	N
vg0910357999	T -> C	LOC_Os09g16930.1	upstream_gene_variant ; 793.0bp to feature; MODIFIER	N	Average:11.889; most accessible tissue: Zhenshan97 flag leaf, score: 17.069	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910357999	1.30E-06	NA	mr1800_2	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