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Detailed information for vg0506481904:

Variant ID: vg0506481904 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6481904
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAACATATTTTAAGTAGATAAATGAGGAGAGAGAAGAGCAACGGGCTACAGATTTGTAGCCAGCTGTAGCACGAACTCCAAGATACAGTGTGTGTATGA[T/C]
AAGTGGGACCATGTATTTATAGTGTAGTATGTAACTATTGTATAAATGAGCTATCAGATTGGTTATAGATGAATTGGAGCTAGTAGTTGGCTGTACTATT

Reverse complement sequence

AATAGTACAGCCAACTACTAGCTCCAATTCATCTATAACCAATCTGATAGCTCATTTATACAATAGTTACATACTACACTATAAATACATGGTCCCACTT[A/G]
TCATACACACACTGTATCTTGGAGTTCGTGCTACAGCTGGCTACAAATCTGTAGCCCGTTGCTCTTCTCTCTCCTCATTTATCTACTTAAAATATGTTTG

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	85.40%	11.80%	2.77%	0.00%	NA
All Indica	2759	95.30%	1.80%	2.90%	0.00%	NA
All Japonica	1512	64.00%	32.70%	3.31%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	88.20%	4.00%	7.73%	0.00%	NA
Indica II	465	95.30%	1.90%	2.80%	0.00%	NA
Indica III	913	99.60%	0.30%	0.11%	0.00%	NA
Indica Intermediate	786	95.50%	1.90%	2.54%	0.00%	NA
Temperate Japonica	767	34.20%	61.40%	4.43%	0.00%	NA
Tropical Japonica	504	98.60%	0.80%	0.60%	0.00%	NA
Japonica Intermediate	241	86.30%	8.30%	5.39%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	13.30%	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
vg0506481904	T -> C	LOC_Os05g11460.1	downstream_gene_variant ; 2150.0bp to feature; MODIFIER	silent_mutation	Average:45.508; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg0506481904	T -> C	LOC_Os05g11428-LOC_Os05g11460	intergenic_region ; MODIFIER	silent_mutation	Average:45.508; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506481904	NA	6.33E-06	mr1639	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
vg0506481904	4.65E-06	NA	mr1648	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
vg0506481904	NA	4.03E-08	mr1648	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