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Detailed information for vg0716086571:

Variant ID: vg0716086571 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16086571
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: 116. )

Flanking Sequence (100 bp) in Reference Genome:

GGCGAGAAATAAGAACTCGCGCTCATCACCTTCCTCCGCGACAATGCGGATGTGTTCGCTTGGCAGCTGTCCGACATACCGGGGGTCCCCAGGGAGGTGA[T/C]
TGAGCACAAACTCATGGTGCGACCCGACGCCAAGCCAGTAAAGCAAAAACTGTGGAGATTTGCACCAGATCGAAAACAAGCCATACGAGAAGAGCTCGAC

Reverse complement sequence

GTCGAGCTCTTCTCGTATGGCTTGTTTTCGATCTGGTGCAAATCTCCACAGTTTTTGCTTTACTGGCTTGGCGTCGGGTCGCACCATGAGTTTGTGCTCA[A/G]
TCACCTCCCTGGGGACCCCCGGTATGTCGGACAGCTGCCAAGCGAACACATCCGCATTGTCGCGGAGGAAGGTGATGAGCGCGAGTTCTTATTTCTCGCC

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	47.10%	19.10%	2.12%	31.61%	NA
All Indica	2759	15.70%	30.00%	2.21%	52.08%	NA
All Japonica	1512	99.40%	0.10%	0.07%	0.46%	NA
Aus	269	53.20%	23.40%	13.75%	9.67%	NA
Indica I	595	6.90%	51.60%	1.01%	40.50%	NA
Indica II	465	13.10%	13.80%	3.23%	69.89%	NA
Indica III	913	14.90%	22.00%	3.07%	60.02%	NA
Indica Intermediate	786	24.70%	32.70%	1.53%	41.09%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	99.60%	0.20%	0.00%	0.20%	NA
Japonica Intermediate	241	98.80%	0.00%	0.41%	0.83%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	62.20%	10.00%	1.11%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0716086571	T -> DEL	LOC_Os07g27520.1	N	frameshift_variant	Average:10.02; most accessible tissue: Callus, score: 21.197	N	N	N	N
vg0716086571	T -> C	LOC_Os07g27520.1	missense_variant ; p.Ile721Thr; MODERATE	nonsynonymous_codon ; I721T	Average:10.02; most accessible tissue: Callus, score: 21.197	benign	0.149	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716086571	NA	5.32E-09	mr1575	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
vg0716086571	1.59E-06	1.59E-06	mr1575	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