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Detailed information for vg0418844692:

Variant ID: vg0418844692 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 18844692
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGAAATCTGGTTGGCACTTCCGAGAGGGCTTAGAGATGGAGGAGGGGTTTTTCAGCCTCTAGTTCATTTTTCAGCTTAAAAATCTTAAACTCTCCCAAA[C/T]
AAGATCTAGTTTATTTTCCACGATCTACATCTACATATTGTAAAAATCTAAGTAACAATCTGGACTGTTTGAGGGAGCTGAAGATTTTGTGGGAAGCTGC

Reverse complement sequence

GCAGCTTCCCACAAAATCTTCAGCTCCCTCAAACAGTCCAGATTGTTACTTAGATTTTTACAATATGTAGATGTAGATCGTGGAAAATAAACTAGATCTT[G/A]
TTTGGGAGAGTTTAAGATTTTTAAGCTGAAAAATGAACTAGAGGCTGAAAAACCCCTCCTCCATCTCTAAGCCCTCTCGGAAGTGCCAACCAGATTTCAC

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	80.50%	19.50%	0.02%	0.00%	NA
All Indica	2759	71.90%	28.10%	0.00%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	49.40%	50.20%	0.37%	0.00%	NA
Indica I	595	55.00%	45.00%	0.00%	0.00%	NA
Indica II	465	90.80%	9.20%	0.00%	0.00%	NA
Indica III	913	70.20%	29.80%	0.00%	0.00%	NA
Indica Intermediate	786	75.60%	24.40%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0418844692	C -> T	LOC_Os04g31510.1	upstream_gene_variant ; 2395.0bp to feature; MODIFIER	silent_mutation	Average:38.957; most accessible tissue: Callus, score: 67.202	N	N	N	N
vg0418844692	C -> T	LOC_Os04g31520.1	upstream_gene_variant ; 1570.0bp to feature; MODIFIER	silent_mutation	Average:38.957; most accessible tissue: Callus, score: 67.202	N	N	N	N
vg0418844692	C -> T	LOC_Os04g31524.1	downstream_gene_variant ; 2328.0bp to feature; MODIFIER	silent_mutation	Average:38.957; most accessible tissue: Callus, score: 67.202	N	N	N	N
vg0418844692	C -> T	LOC_Os04g31510-LOC_Os04g31520	intergenic_region ; MODIFIER	silent_mutation	Average:38.957; most accessible tissue: Callus, score: 67.202	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0418844692	1.72E-06	NA	mr1141	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