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Detailed information for vg0216418368:

Variant ID: vg0216418368 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 16418368
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACTATTAATGCCGAGGAAGATGGTTTATCATGAAATTTTGTTCCATGTGCGGTGGCGATTAGTTTCTGTCTCTCCAAACACCATGAAGGCGAGCAGTCT[C/T]
GAGGAGCCGGGAAGCATGGGAGGCGCGCAGGAGGTGGGGAGCCGGCGGGTCGGTCACCATTCTAGCAGTGCCGGCAGATGCGAACGCTTGGGAGTCAAGA

Reverse complement sequence

TCTTGACTCCCAAGCGTTCGCATCTGCCGGCACTGCTAGAATGGTGACCGACCCGCCGGCTCCCCACCTCCTGCGCGCCTCCCATGCTTCCCGGCTCCTC[G/A]
AGACTGCTCGCCTTCATGGTGTTTGGAGAGACAGAAACTAATCGCCACCGCACATGGAACAAAATTTCATGATAAACCATCTTCCTCGGCATTAATAGTC

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	99.00%	0.80%	0.19%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	97.10%	2.40%	0.53%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	96.10%	3.10%	0.78%	0.00%	NA
Tropical Japonica	504	98.80%	1.00%	0.20%	0.00%	NA
Japonica Intermediate	241	96.70%	2.90%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	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
vg0216418368	C -> T	LOC_Os02g27720.1	upstream_gene_variant ; 824.0bp to feature; MODIFIER	silent_mutation	Average:60.003; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N
vg0216418368	C -> T	LOC_Os02g27710.1	downstream_gene_variant ; 2706.0bp to feature; MODIFIER	silent_mutation	Average:60.003; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N
vg0216418368	C -> T	LOC_Os02g27710-LOC_Os02g27720	intergenic_region ; MODIFIER	silent_mutation	Average:60.003; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0216418368	5.31E-06	5.30E-06	mr1014	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
vg0216418368	1.73E-06	1.73E-06	mr1015	Jap_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
vg0216418368	8.09E-06	NA	mr1159	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