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Detailed information for vg0826865048:

Variant ID: vg0826865048 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 26865048
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGGACAATTATATCAAAGGTCCGTTGTATGTTGTCTAATGCAGGTTTGCCCAAACAGTTTTGGGCGGAAGCCATTTCCATTGCTTGTTATCTTATCAAT[T/C]
GGTCACCCAGTTATGCCATTGATAAGAAGACTCCAATTGAGGTATGGTCTGGTTCCCCAGCAAATTATTCAGATTTAAGAGTATTTGGTTATACTACTTA

Reverse complement sequence

TAAGTAGTATAACCAAATACTCTTAAATCTGAATAATTTGCTGGGGAACCAGACCATACCTCAATTGGAGTCTTCTTATCAATGGCATAACTGGGTGACC[A/G]
ATTGATAAGATAACAAGCAATGGAAATGGCTTCCGCCCAAAACTGTTTGGGCAAACCTGCATTAGACAACATACAACGGACCTTTGATATAATTGTCCTA

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	72.80%	27.20%	0.02%	0.00%	NA
All Indica	2759	98.60%	1.40%	0.00%	0.00%	NA
All Japonica	1512	35.00%	64.90%	0.07%	0.00%	NA
Aus	269	43.50%	56.50%	0.00%	0.00%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	98.80%	1.20%	0.00%	0.00%	NA
Indica Intermediate	786	97.50%	2.50%	0.00%	0.00%	NA
Temperate Japonica	767	12.00%	88.00%	0.00%	0.00%	NA
Tropical Japonica	504	61.90%	37.90%	0.20%	0.00%	NA
Japonica Intermediate	241	51.90%	48.10%	0.00%	0.00%	NA
VI/Aromatic	96	8.30%	91.70%	0.00%	0.00%	NA
Intermediate	90	71.10%	28.90%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0826865048	T -> C	LOC_Os08g42500.1	missense_variant ; p.Trp373Arg; MODERATE	nonsynonymous_codon ; W373R	Average:21.055; most accessible tissue: Callus, score: 44.88	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0826865048	6.41E-06	1.29E-09	mr1364	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
vg0826865048	3.64E-06	1.72E-09	mr1443	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