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Detailed information for vg0624947878:

Variant ID: vg0624947878 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 24947878
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCTTTGAGTTGCTTCATATTATTGAAGGCTACCTTAGGAATGTCTCTCAAATGATCTACGTAGATCTTCAGCTTTTCAACAAACTCTAGGTGATGAACA[C/T]
GCAAGACATAGAAGAAGCTTGACAACAGGCAGCAAAATGATCTTGTGAGTTCAAAGTTGTCCATAAAAACCTTGAAGTGGATTTGTTCCTTATCAAGTAT

Reverse complement sequence

ATACTTGATAAGGAACAAATCCACTTCAAGGTTTTTATGGACAACTTTGAACTCACAAGATCATTTTGCTGCCTGTTGTCAAGCTTCTTCTATGTCTTGC[G/A]
TGTTCATCACCTAGAGTTTGTTGAAAAGCTGAAGATCTACGTAGATCATTTGAGAGACATTCCTAAGGTAGCCTTCAATAATATGAAGCAACTCAAAGAG

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	98.50%	1.50%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	95.60%	4.40%	0.00%	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	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	87.30%	12.70%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0624947878	C -> T	LOC_Os06g41660.1	upstream_gene_variant ; 2598.0bp to feature; MODIFIER	silent_mutation	Average:40.69; most accessible tissue: Zhenshan97 flower, score: 50.724	N	N	N	N
vg0624947878	C -> T	LOC_Os06g41660-LOC_Os06g41670	intergenic_region ; MODIFIER	silent_mutation	Average:40.69; most accessible tissue: Zhenshan97 flower, score: 50.724	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0624947878	3.04E-07	NA	mr1817	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
vg0624947878	NA	5.32E-06	mr1723_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