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Detailed information for vg0228836104:

Variant ID: vg0228836104 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 28836104
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTGCTCGATAGGCATTCTACGTTTTCCTTCCGAGATCACATTGTGACTTGATTACGCATAGGCTCTTCCTCTGACTGACATCATCGGGCTGCTCGCGGA[C/T]
CATCAGGTGGTGGCGTCTTTGAAAGAGAAGGTCGCCAATGAGGCGTCTGATGCTGCTGCTGCTACTACTACAAGTGGTGGCAATGTTCCGACAAAGGGGA

Reverse complement sequence

TCCCCTTTGTCGGAACATTGCCACCACTTGTAGTAGTAGCAGCAGCAGCATCAGACGCCTCATTGGCGACCTTCTCTTTCAAAGACGCCACCACCTGATG[G/A]
TCCGCGAGCAGCCCGATGATGTCAGTCAGAGGAAGAGCCTATGCGTAATCAAGTCACAATGTGATCTCGGAAGGAAAACGTAGAATGCCTATCGAGCACA

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	61.30%	33.90%	4.57%	0.25%	NA
All Indica	2759	35.50%	56.60%	7.54%	0.36%	NA
All Japonica	1512	99.60%	0.30%	0.07%	0.00%	NA
Aus	269	89.60%	8.90%	0.74%	0.74%	NA
Indica I	595	27.40%	60.00%	11.26%	1.34%	NA
Indica II	465	44.50%	54.40%	1.08%	0.00%	NA
Indica III	913	33.70%	54.50%	11.72%	0.00%	NA
Indica Intermediate	786	38.30%	57.80%	3.69%	0.25%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	13.30%	5.56%	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
vg0228836104	C -> T	LOC_Os02g47250.1	synonymous_variant ; p.Asp88Asp; LOW	synonymous_codon	Average:42.181; most accessible tissue: Zhenshan97 flower, score: 55.587	N	N	N	N
vg0228836104	C -> DEL	LOC_Os02g47250.1	N	frameshift_variant	Average:42.181; most accessible tissue: Zhenshan97 flower, score: 55.587	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0228836104	NA	2.19E-12	mr1734_2	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