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Detailed information for vg0615088161:

Variant ID: vg0615088161 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 15088161
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCTTCATTTGGAGATGAGTGAATGCTAGGAATGTCTTCATTAACTAGTCGGCGGCGGACGAGGCAGCCGGTCGGTGAGGATGTAGACGCCCAACAACGG[C/T]
GGCATAATAGGCCAGCCATGCAGGCGGAAACACCAGTCGGCGGCGGACGAGGCGACCGGTCGGTGAAGACGTAGACGCTCAACAACAGTGGCATAATAGG

Reverse complement sequence

CCTATTATGCCACTGTTGTTGAGCGTCTACGTCTTCACCGACCGGTCGCCTCGTCCGCCGCCGACTGGTGTTTCCGCCTGCATGGCTGGCCTATTATGCC[G/A]
CCGTTGTTGGGCGTCTACATCCTCACCGACCGGCTGCCTCGTCCGCCGCCGACTAGTTAATGAAGACATTCCTAGCATTCACTCATCTCCAAATGAAGCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.80%	4.50%	1.80%	4.89%	NA
All Indica	2759	89.60%	7.20%	2.94%	0.25%	NA
All Japonica	1512	99.70%	0.10%	0.00%	0.13%	NA
Aus	269	33.80%	4.10%	0.37%	61.71%	NA
Indica I	595	89.20%	7.10%	3.70%	0.00%	NA
Indica II	465	88.80%	6.70%	4.52%	0.00%	NA
Indica III	913	93.30%	5.80%	0.77%	0.11%	NA
Indica Intermediate	786	85.90%	9.40%	3.94%	0.76%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	44.80%	2.10%	3.12%	50.00%	NA
Intermediate	90	91.10%	0.00%	0.00%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0615088161	C -> T	LOC_Os06g25830.1	missense_variant ; p.Arg170His; MODERATE	nonsynonymous_codon ; R170H	Average:34.298; most accessible tissue: Minghui63 panicle, score: 59.629	benign	0.707	TOLERATED	0.20
vg0615088161	C -> DEL	LOC_Os06g25830.1	N	frameshift_variant	Average:34.298; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0615088161	2.80E-06	2.80E-06	mr1875	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