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Detailed information for vg0400898122:

Variant ID: vg0400898122 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 898122
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTCATATCATTTGATTCATTGTTAAATATACTTATATGTATACATATACTTTTACTTATTTCACAAAAGTTTTTGAATAAGACGAACGGTCAAACATGT[G/A]
ATAAAAAGTTAACGGTGTCAAAAATATTTAGAGACGGAAGGAGTACTACTTTTATCTCCCCCAGTCCTGAAACTTCTTGTGGTGAAGGTGGAGGAGGGGG

Reverse complement sequence

CCCCCTCCTCCACCTTCACCACAAGAAGTTTCAGGACTGGGGGAGATAAAAGTAGTACTCCTTCCGTCTCTAAATATTTTTGACACCGTTAACTTTTTAT[C/T]
ACATGTTTGACCGTTCGTCTTATTCAAAAACTTTTGTGAAATAAGTAAAAGTATATGTATACATATAAGTATATTTAACAATGAATCAAATGATATGAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.00%	6.80%	1.14%	3.05%	NA
All Indica	2759	97.20%	0.20%	0.07%	2.54%	NA
All Japonica	1512	72.20%	20.00%	3.24%	4.63%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	89.20%	0.20%	0.00%	10.54%	NA
Indica III	913	99.60%	0.10%	0.11%	0.22%	NA
Indica Intermediate	786	97.20%	0.30%	0.13%	2.42%	NA
Temperate Japonica	767	77.60%	22.30%	0.13%	0.00%	NA
Tropical Japonica	504	56.00%	21.60%	8.73%	13.69%	NA
Japonica Intermediate	241	88.80%	9.10%	1.66%	0.41%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	82.20%	10.00%	3.33%	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
vg0400898122	G -> DEL	N	N	silent_mutation	Average:40.022; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0400898122	G -> A	LOC_Os04g02460.1	upstream_gene_variant ; 3523.0bp to feature; MODIFIER	silent_mutation	Average:40.022; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0400898122	G -> A	LOC_Os04g02470.1	downstream_gene_variant ; 2133.0bp to feature; MODIFIER	silent_mutation	Average:40.022; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0400898122	G -> A	LOC_Os04g02480.1	downstream_gene_variant ; 884.0bp to feature; MODIFIER	silent_mutation	Average:40.022; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0400898122	G -> A	LOC_Os04g02490.1	downstream_gene_variant ; 1683.0bp to feature; MODIFIER	silent_mutation	Average:40.022; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0400898122	G -> A	LOC_Os04g02470-LOC_Os04g02480	intergenic_region ; MODIFIER	silent_mutation	Average:40.022; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400898122	3.96E-06	NA	mr1454	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