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Detailed information for vg0503604454:

Variant ID: vg0503604454 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 3604454
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTCGCTGCCCATTTGCAGGCGGCCCCCCGCACAGTACAAAATCGCCCTAGCGGAGGGCAGCAAGGGGGCCGCCTGCAAATTTCGTTGACGGCCGTCGCC[C/T]
GAGAGCGAACAGCCGTCTGCCACGTCACTTTCGCCGCCCTTTGGGATGGCGATTTTTAAGGCGACTACTTCTGTCAATTTTCAAAATGGAAAATTATTTT

Reverse complement sequence

AAAATAATTTTCCATTTTGAAAATTGACAGAAGTAGTCGCCTTAAAAATCGCCATCCCAAAGGGCGGCGAAAGTGACGTGGCAGACGGCTGTTCGCTCTC[G/A]
GGCGACGGCCGTCAACGAAATTTGCAGGCGGCCCCCTTGCTGCCCTCCGCTAGGGCGATTTTGTACTGTGCGGGGGGCCGCCTGCAAATGGGCAGCGAGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.10%	43.80%	0.06%	0.00%	NA
All Indica	2759	90.70%	9.20%	0.07%	0.00%	NA
All Japonica	1512	1.70%	98.30%	0.07%	0.00%	NA
Aus	269	12.30%	87.70%	0.00%	0.00%	NA
Indica I	595	98.20%	1.80%	0.00%	0.00%	NA
Indica II	465	94.40%	5.60%	0.00%	0.00%	NA
Indica III	913	86.40%	13.60%	0.00%	0.00%	NA
Indica Intermediate	786	87.80%	12.00%	0.25%	0.00%	NA
Temperate Japonica	767	1.80%	98.20%	0.00%	0.00%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.50%	0.41%	0.00%	NA
VI/Aromatic	96	61.50%	38.50%	0.00%	0.00%	NA
Intermediate	90	36.70%	63.30%	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
vg0503604454	C -> T	LOC_Os05g06870.1	upstream_gene_variant ; 2763.0bp to feature; MODIFIER	silent_mutation	Average:37.57; most accessible tissue: Minghui63 root, score: 54.099	N	N	N	N
vg0503604454	C -> T	LOC_Os05g06890.1	upstream_gene_variant ; 3048.0bp to feature; MODIFIER	silent_mutation	Average:37.57; most accessible tissue: Minghui63 root, score: 54.099	N	N	N	N
vg0503604454	C -> T	LOC_Os05g06880.1	downstream_gene_variant ; 766.0bp to feature; MODIFIER	silent_mutation	Average:37.57; most accessible tissue: Minghui63 root, score: 54.099	N	N	N	N
vg0503604454	C -> T	LOC_Os05g06880-LOC_Os05g06890	intergenic_region ; MODIFIER	silent_mutation	Average:37.57; most accessible tissue: Minghui63 root, score: 54.099	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0503604454	NA	1.22E-06	mr1321	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
vg0503604454	3.44E-06	3.44E-06	mr1612	Ind_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