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Detailed information for vg0907107754:

Variant ID: vg0907107754 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7107754
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.03, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TCATAACTAAATAAATAAATCATAGGAAGAAATGAGTTAATCACTTGACACTTAGTAAAACATATATCAGACAACAAGATGATTCTAGTAAGAAACATTG[T/C]
GTTACAGGTCACACCTGTTCTGTTGCCTAGGCACTTTTGGAAACTCGTACTCCCAAGAGAAAAAACAGAACGCAACATCCATGGTTTTGTTAAGAGCACC

Reverse complement sequence

GGTGCTCTTAACAAAACCATGGATGTTGCGTTCTGTTTTTTCTCTTGGGAGTACGAGTTTCCAAAAGTGCCTAGGCAACAGAACAGGTGTGACCTGTAAC[A/G]
CAATGTTTCTTACTAGAATCATCTTGTTGTCTGATATATGTTTTACTAAGTGTCAAGTGATTAACTCATTTCTTCCTATGATTTATTTATTTAGTTATGA

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	80.20%	9.70%	0.23%	9.84%	NA
All Indica	2759	72.60%	16.30%	0.18%	10.91%	NA
All Japonica	1512	89.00%	0.40%	0.40%	10.25%	NA
Aus	269	98.90%	0.00%	0.00%	1.12%	NA
Indica I	595	49.40%	49.20%	0.17%	1.18%	NA
Indica II	465	91.20%	5.80%	0.00%	3.01%	NA
Indica III	913	70.80%	2.00%	0.00%	27.27%	NA
Indica Intermediate	786	81.20%	14.40%	0.51%	3.94%	NA
Temperate Japonica	767	98.40%	0.00%	0.13%	1.43%	NA
Tropical Japonica	504	85.30%	0.80%	0.60%	13.29%	NA
Japonica Intermediate	241	66.40%	0.80%	0.83%	31.95%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	3.30%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0907107754	T -> DEL	N	N	silent_mutation	Average:53.999; most accessible tissue: Zhenshan97 flower, score: 76.539	N	N	N	N
vg0907107754	T -> C	LOC_Os09g12420.1	intron_variant ; MODIFIER	silent_mutation	Average:53.999; most accessible tissue: Zhenshan97 flower, score: 76.539	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907107754	NA	2.97E-08	mr1610	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
vg0907107754	NA	3.19E-06	mr1914	Ind_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
vg0907107754	NA	1.02E-10	mr1927	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
vg0907107754	NA	5.23E-07	mr1927	Ind_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