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Detailed information for vg0616901911:

Variant ID: vg0616901911 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 16901911
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTGAGGGGTTATCCACCAAAGCCCATGAGAAAATTCGGAGCAAAATGGGCCAGAAAGGGTTTGGCTGAACCAAGTGGTTCGGCCGAACCCCTAGCTGTG[C/T]
CGTTCAGCCCCAAACTTCACAGGCCGGCAGTTACTGACTTGCTATGACGGTTTCTACCGACTTTACCTGAATAACCGTCATCAGCTGGACACATGGCACT

Reverse complement sequence

AGTGCCATGTGTCCAGCTGATGACGGTTATTCAGGTAAAGTCGGTAGAAACCGTCATAGCAAGTCAGTAACTGCCGGCCTGTGAAGTTTGGGGCTGAACG[G/A]
CACAGCTAGGGGTTCGGCCGAACCACTTGGTTCAGCCAAACCCTTTCTGGCCCATTTTGCTCCGAATTTTCTCATGGGCTTTGGTGGATAACCCCTCAGC

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	97.90%	1.90%	0.17%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	94.50%	5.00%	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	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.50%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	86.70%	12.70%	0.60%	0.00%	NA
Japonica Intermediate	241	93.80%	4.10%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0616901911	C -> T	LOC_Os06g29480.1	upstream_gene_variant ; 1037.0bp to feature; MODIFIER	silent_mutation	Average:52.378; most accessible tissue: Minghui63 young leaf, score: 75.479	N	N	N	N
vg0616901911	C -> T	LOC_Os06g29470.1	downstream_gene_variant ; 4250.0bp to feature; MODIFIER	silent_mutation	Average:52.378; most accessible tissue: Minghui63 young leaf, score: 75.479	N	N	N	N
vg0616901911	C -> T	LOC_Os06g29470-LOC_Os06g29480	intergenic_region ; MODIFIER	silent_mutation	Average:52.378; most accessible tissue: Minghui63 young leaf, score: 75.479	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0616901911	7.29E-07	2.33E-09	mr1218_2	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
vg0616901911	NA	2.36E-08	mr1850_2	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