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Detailed information for vg0712504916:

Variant ID: vg0712504916 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 12504916
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.30, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

AGTCACAACATATCCAAGAAATGAAACTCGTTCCGTGCAAAAGATGCACTTTTCAAGGTTAGCAAACAAACGTGCATCGCGTAGAGCATTAAAAACAGCA[T/C]
GTAAATGATCCATGTGTTCATCCAAAGACTTGCTGTAAATCAATATGTCATCAAAGTAAACTACCACAAATCGTCCAATAAAAGGCCTTAAAACCTCATT

Reverse complement sequence

AATGAGGTTTTAAGGCCTTTTATTGGACGATTTGTGGTAGTTTACTTTGATGACATATTGATTTACAGCAAGTCTTTGGATGAACACATGGATCATTTAC[A/G]
TGCTGTTTTTAATGCTCTACGCGATGCACGTTTGTTTGCTAACCTTGAAAAGTGCATCTTTTGCACGGAACGAGTTTCATTTCTTGGATATGTTGTGACT

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	36.30%	1.50%	2.26%	59.94%	NA
All Indica	2759	11.70%	0.90%	1.92%	85.54%	NA
All Japonica	1512	79.80%	0.00%	1.65%	18.52%	NA
Aus	269	22.70%	16.00%	7.43%	53.90%	NA
Indica I	595	10.80%	0.70%	1.18%	87.39%	NA
Indica II	465	11.80%	0.20%	1.29%	86.67%	NA
Indica III	913	8.90%	1.10%	2.30%	87.73%	NA
Indica Intermediate	786	15.50%	1.10%	2.42%	80.92%	NA
Temperate Japonica	767	67.10%	0.00%	2.87%	29.99%	NA
Tropical Japonica	504	98.60%	0.00%	0.20%	1.19%	NA
Japonica Intermediate	241	80.90%	0.00%	0.83%	18.26%	NA
VI/Aromatic	96	79.20%	0.00%	8.33%	12.50%	NA
Intermediate	90	55.60%	3.30%	1.11%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0712504916	T -> DEL	LOC_Os07g22310.1	N	frameshift_variant	Average:29.054; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0712504916	T -> C	LOC_Os07g22310.1	missense_variant ; p.His1131Arg; MODERATE	nonsynonymous_codon ; H1131R	Average:29.054; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	benign	-0.752	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0712504916	1.17E-06	5.47E-07	mr1263	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
vg0712504916	1.17E-06	5.47E-07	mr1451	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