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Detailed information for vg0225037217:

Variant ID: vg0225037217 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 25037217
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCTGCCTTTGTGGCCTCCGAGCCAATGTCGGGGGTGGCCGGGCTAACTTCGCCGCTAACCTCTTTTACTGATGGCTTCGTCAGGATGTCTAGAAAAGTG[T/C]
CGGGTTCGAGCGGTTCTCGTCTGGACGCACGTCGTGCTAGGTCATCTAGCTCGATGTTGTCCTTGCGGTAAACGTGTCGGACCTCGATCCCATCGAACCT

Reverse complement sequence

AGGTTCGATGGGATCGAGGTCCGACACGTTTACCGCAAGGACAACATCGAGCTAGATGACCTAGCACGACGTGCGTCCAGACGAGAACCGCTCGAACCCG[A/G]
CACTTTTCTAGACATCCTGACGAAGCCATCAGTAAAAGAGGTTAGCGGCGAAGTTAGCCCGGCCACCCCCGACATTGGCTCGGAGGCCACAAAGGCAGAA

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	83.30%	14.90%	0.19%	1.61%	NA
All Indica	2759	94.80%	2.20%	0.25%	2.75%	NA
All Japonica	1512	59.50%	40.40%	0.13%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	96.80%	2.90%	0.34%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	91.30%	0.40%	0.33%	7.89%	NA
Indica Intermediate	786	94.40%	4.80%	0.25%	0.51%	NA
Temperate Japonica	767	39.20%	60.50%	0.26%	0.00%	NA
Tropical Japonica	504	92.30%	7.70%	0.00%	0.00%	NA
Japonica Intermediate	241	55.20%	44.80%	0.00%	0.00%	NA
VI/Aromatic	96	81.20%	18.80%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg0225037217	T -> DEL	LOC_Os02g41696.1	N	frameshift_variant	Average:33.973; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg0225037217	T -> C	LOC_Os02g41696.1	missense_variant ; p.Asp131Gly; MODERATE	nonsynonymous_codon ; D131G	Average:33.973; most accessible tissue: Zhenshan97 root, score: 39.742	benign	-0.481	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0225037217	NA	6.63E-08	mr1617	Jap_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
vg0225037217	3.46E-06	3.47E-06	mr1994	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