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Detailed information for vg0404559892:

Variant ID: vg0404559892 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4559892
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAGAGCCTTGACGGCTTGTTTGGTAACTCGAGGAAAGACGATTGGAAGTTTATATGAGGGAATTGATGATGAGATTAAGATGAGAATTTGATTTTTAAT[C/T]
CCAATATCTTGTTTGGTAGAGATGATGGAAATTGATAGGTAATTTAGTTGGAGATTAGGTCATTAATAAAAACGGATGGCTGAGATTTGCTTACACAAAG

Reverse complement sequence

CTTTGTGTAAGCAAATCTCAGCCATCCGTTTTTATTAATGACCTAATCTCCAACTAAATTACCTATCAATTTCCATCATCTCTACCAAACAAGATATTGG[G/A]
ATTAAAAATCAAATTCTCATCTTAATCTCATCATCAATTCCCTCATATAAACTTCCAATCGTCTTTCCTCGAGTTACCAAACAAGCCGTCAAGGCTCTGT

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	86.40%	3.50%	0.00%	10.14%	NA
All Indica	2759	83.10%	0.30%	0.00%	16.53%	NA
All Japonica	1512	92.90%	6.90%	0.00%	0.13%	NA
Aus	269	92.90%	1.10%	0.00%	5.95%	NA
Indica I	595	46.40%	0.00%	0.00%	53.61%	NA
Indica II	465	92.50%	0.20%	0.00%	7.31%	NA
Indica III	913	97.00%	0.50%	0.00%	2.41%	NA
Indica Intermediate	786	89.30%	0.40%	0.00%	10.31%	NA
Temperate Japonica	767	94.50%	5.50%	0.00%	0.00%	NA
Tropical Japonica	504	88.30%	11.50%	0.00%	0.20%	NA
Japonica Intermediate	241	97.50%	2.10%	0.00%	0.41%	NA
VI/Aromatic	96	53.10%	45.80%	0.00%	1.04%	NA
Intermediate	90	92.20%	3.30%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404559892	C -> DEL	N	N	silent_mutation	Average:51.034; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N
vg0404559892	C -> T	LOC_Os04g08460.1	downstream_gene_variant ; 611.0bp to feature; MODIFIER	silent_mutation	Average:51.034; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N
vg0404559892	C -> T	LOC_Os04g08470.1	downstream_gene_variant ; 4511.0bp to feature; MODIFIER	silent_mutation	Average:51.034; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N
vg0404559892	C -> T	LOC_Os04g08460-LOC_Os04g08470	intergenic_region ; MODIFIER	silent_mutation	Average:51.034; most accessible tissue: Minghui63 panicle, score: 79.811	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404559892	1.09E-06	1.45E-06	mr1549_2	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