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Detailed information for vg0515257168:

Variant ID: vg0515257168 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 15257168
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTGGAGATAGAACTGTGTAGCCGGGATGGTTGTTCAGAATGGTTGGGCCTATGCAACAGGGTATGTTGTATAGCGTTGGTTTAATATTGTTTAATTAT[T/C]
ACTTAACGGTTTTATTAAATTCTGAAATATTTATTAAATGCTGTTTATGCAAATGAAACCCTACTATGCCATCGTTTGTTATCCTGTGCACTTGCATATT

Reverse complement sequence

AATATGCAAGTGCACAGGATAACAAACGATGGCATAGTAGGGTTTCATTTGCATAAACAGCATTTAATAAATATTTCAGAATTTAATAAAACCGTTAAGT[A/G]
ATAATTAAACAATATTAAACCAACGCTATACAACATACCCTGTTGCATAGGCCCAACCATTCTGAACAACCATCCCGGCTACACAGTTCTATCTCCAAAC

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	88.20%	1.10%	5.37%	5.37%	NA
All Indica	2759	84.90%	1.90%	8.23%	5.00%	NA
All Japonica	1512	92.20%	0.00%	1.32%	6.48%	NA
Aus	269	94.10%	0.00%	2.60%	3.35%	NA
Indica I	595	71.80%	1.20%	15.97%	11.09%	NA
Indica II	465	90.10%	1.90%	4.30%	3.66%	NA
Indica III	913	92.80%	1.80%	4.27%	1.20%	NA
Indica Intermediate	786	82.60%	2.50%	9.29%	5.60%	NA
Temperate Japonica	767	96.20%	0.00%	0.39%	3.39%	NA
Tropical Japonica	504	85.90%	0.00%	2.98%	11.11%	NA
Japonica Intermediate	241	92.50%	0.00%	0.83%	6.64%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	0.00%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0515257168	T -> DEL	N	N	silent_mutation	Average:18.038; most accessible tissue: Minghui63 young leaf, score: 27.355	N	N	N	N
vg0515257168	T -> C	LOC_Os05g26230.1	upstream_gene_variant ; 2012.0bp to feature; MODIFIER	silent_mutation	Average:18.038; most accessible tissue: Minghui63 young leaf, score: 27.355	N	N	N	N
vg0515257168	T -> C	LOC_Os05g26220.1	intron_variant ; MODIFIER	silent_mutation	Average:18.038; most accessible tissue: Minghui63 young leaf, score: 27.355	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0515257168	1.75E-06	1.75E-06	mr1340	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
vg0515257168	2.18E-06	2.18E-06	mr1381	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
vg0515257168	3.92E-06	3.92E-06	mr1957	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