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Detailed information for vg0908891812:

Variant ID: vg0908891812 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 8891812
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

AGCTTCAGTTCTGAAACTCTAGAATAGTAATACAAACCAATTAATTACTTGATAACTTTAGTTCCGAAACTCAATATTTTCATAATAAACAGTGCCTTGG[T/C]
CAAGAACTTGACAATGATTTTGAGAAGGTTGCCACTAGCAGGAATACTGAAGAAATTTGCAATGACAAGGAGTTGAAGATTCTCAATGGATCATCTGTTC

Reverse complement sequence

GAACAGATGATCCATTGAGAATCTTCAACTCCTTGTCATTGCAAATTTCTTCAGTATTCCTGCTAGTGGCAACCTTCTCAAAATCATTGTCAAGTTCTTG[A/G]
CCAAGGCACTGTTTATTATGAAAATATTGAGTTTCGGAACTAAAGTTATCAAGTAATTAATTGGTTTGTATTACTATTCTAGAGTTTCAGAACTGAAGCT

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	64.10%	20.90%	3.07%	11.93%	NA
All Indica	2759	41.10%	35.40%	4.64%	18.88%	NA
All Japonica	1512	97.40%	0.10%	0.26%	2.25%	NA
Aus	269	96.30%	0.40%	1.49%	1.86%	NA
Indica I	595	33.30%	28.20%	5.55%	32.94%	NA
Indica II	465	66.70%	15.30%	3.66%	14.41%	NA
Indica III	913	30.60%	49.00%	5.37%	15.12%	NA
Indica Intermediate	786	44.10%	36.90%	3.69%	15.27%	NA
Temperate Japonica	767	99.50%	0.00%	0.26%	0.26%	NA
Tropical Japonica	504	93.80%	0.40%	0.00%	5.75%	NA
Japonica Intermediate	241	97.90%	0.00%	0.83%	1.24%	NA
VI/Aromatic	96	90.60%	1.00%	7.29%	1.04%	NA
Intermediate	90	86.70%	7.80%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0908891812	T -> DEL	N	N	silent_mutation	Average:28.611; most accessible tissue: Minghui63 root, score: 57.225	N	N	N	N
vg0908891812	T -> C	LOC_Os09g14890.1	upstream_gene_variant ; 1677.0bp to feature; MODIFIER	silent_mutation	Average:28.611; most accessible tissue: Minghui63 root, score: 57.225	N	N	N	N
vg0908891812	T -> C	LOC_Os09g14890-LOC_Os09g14900	intergenic_region ; MODIFIER	silent_mutation	Average:28.611; most accessible tissue: Minghui63 root, score: 57.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0908891812	1.94E-06	1.94E-06	mr1249	Ind_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
vg0908891812	NA	5.64E-08	mr1754_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