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Detailed information for vg0435053623:

Variant ID: vg0435053623 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 35053623
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGTGCAAAAACTTTCTATATGAAAGTTGTTCTAAAATATCATATTACTCTATTTTCCAAGTTTGTAATAATTAAAACTCAATCAATTATACGTTAATAA[C/T]
ACCTCGTTTTACATAAAAAAAACTTAATCTTTATCTTCATCTTCAGGAGAAAAGAACACCACCTAAGATATAGAAAAATATTTAGTAATTTCTCTCCAAA

Reverse complement sequence

TTTGGAGAGAAATTACTAAATATTTTTCTATATCTTAGGTGGTGTTCTTTTCTCCTGAAGATGAAGATAAAGATTAAGTTTTTTTTATGTAAAACGAGGT[G/A]
TTATTAACGTATAATTGATTGAGTTTTAATTATTACAAACTTGGAAAATAGAGTAATATGATATTTTAGAACAACTTTCATATAGAAAGTTTTTGCACAA

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	98.80%	0.90%	0.30%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	96.40%	2.80%	0.86%	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	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	93.20%	5.50%	1.30%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg0435053623	C -> T	LOC_Os04g58920.1	downstream_gene_variant ; 840.0bp to feature; MODIFIER	silent_mutation	Average:70.125; most accessible tissue: Minghui63 root, score: 89.072	N	N	N	N
vg0435053623	C -> T	LOC_Os04g58910-LOC_Os04g58920	intergenic_region ; MODIFIER	silent_mutation	Average:70.125; most accessible tissue: Minghui63 root, score: 89.072	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0435053623	NA	5.89E-06	mr1210	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
vg0435053623	NA	1.48E-06	mr1585	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
vg0435053623	1.39E-06	1.39E-06	mr1899	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