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Detailed information for vg0404517518:

Variant ID: vg0404517518 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4517518
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACCCCCCCCCCTCCTCCCTCCTCCAACCCCCCTCCTATCATAACCGCAATCCCAAACACTAACCCGTATGCTCCTTGCCAAAGTTTGGGGTGTCGTTGG[C/T]
GCCGGAGAAGAAGGGAAGCCTACCGGAATTAGAGGAGAAGAAGTTGACGCGCGAATCTTGGCGTGGATCCAACTGTCCAAAATCTATAAGATTTCATACC

Reverse complement sequence

GGTATGAAATCTTATAGATTTTGGACAGTTGGATCCACGCCAAGATTCGCGCGTCAACTTCTTCTCCTCTAATTCCGGTAGGCTTCCCTTCTTCTCCGGC[G/A]
CCAACGACACCCCAAACTTTGGCAAGGAGCATACGGGTTAGTGTTTGGGATTGCGGTTATGATAGGAGGGGGGTTGGAGGAGGGAGGAGGGGGGGGGGTT

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	88.10%	11.20%	0.25%	0.40%	NA
All Indica	2759	98.70%	1.20%	0.04%	0.07%	NA
All Japonica	1512	73.80%	25.10%	0.60%	0.53%	NA
Aus	269	72.10%	27.90%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	98.10%	1.60%	0.00%	0.22%	NA
Indica Intermediate	786	97.80%	2.20%	0.00%	0.00%	NA
Temperate Japonica	767	93.10%	6.50%	0.39%	0.00%	NA
Tropical Japonica	504	42.10%	55.80%	0.79%	1.39%	NA
Japonica Intermediate	241	78.80%	19.90%	0.83%	0.41%	NA
VI/Aromatic	96	56.20%	32.30%	2.08%	9.38%	NA
Intermediate	90	87.80%	12.20%	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
vg0404517518	C -> DEL	N	N	silent_mutation	Average:71.988; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N
vg0404517518	C -> T	LOC_Os04g08410.1	upstream_gene_variant ; 3635.0bp to feature; MODIFIER	silent_mutation	Average:71.988; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N
vg0404517518	C -> T	LOC_Os04g08415.1	downstream_gene_variant ; 3241.0bp to feature; MODIFIER	silent_mutation	Average:71.988; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N
vg0404517518	C -> T	LOC_Os04g08410-LOC_Os04g08415	intergenic_region ; MODIFIER	silent_mutation	Average:71.988; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404517518	NA	1.32E-07	mr1194	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
vg0404517518	NA	1.31E-06	mr1338	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
vg0404517518	1.03E-07	NA	mr1549_2	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