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Detailed information for vg0623074199:

Variant ID: vg0623074199 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 23074199
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGCACTAGCCATCCTCTGCGCATCTCTTTGCCTTGCACTGGTGGACAGCTCTGACGCAAGGGAAGCTCCGCACAACAGTCCTGAAATTTTTACATTTTG[A/G]
TCCTTTTTGAAAACTTATTTTACAAATAGACCCCAAAAAAACTTAAACCGGAAATGGTCCTTTTTGGGACGCCAGAGTGGCTGGCGCCGTACCCCAACAT

Reverse complement sequence

ATGTTGGGGTACGGCGCCAGCCACTCTGGCGTCCCAAAAAGGACCATTTCCGGTTTAAGTTTTTTTGGGGTCTATTTGTAAAATAAGTTTTCAAAAAGGA[T/C]
CAAAATGTAAAAATTTCAGGACTGTTGTGCGGAGCTTCCCTTGCGTCAGAGCTGTCCACCAGTGCAAGGCAAAGAGATGCGCAGAGGATGGCTAGTGCCA

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	44.80%	24.10%	6.81%	24.29%	NA
All Indica	2759	58.30%	2.80%	10.76%	28.20%	NA
All Japonica	1512	18.80%	68.50%	0.40%	12.30%	NA
Aus	269	31.60%	1.10%	4.83%	62.45%	NA
Indica I	595	53.80%	3.50%	24.71%	17.98%	NA
Indica II	465	66.90%	4.50%	8.60%	20.00%	NA
Indica III	913	55.10%	1.10%	2.30%	41.51%	NA
Indica Intermediate	786	60.30%	3.10%	11.32%	25.32%	NA
Temperate Japonica	767	12.10%	68.70%	0.65%	18.51%	NA
Tropical Japonica	504	28.20%	67.30%	0.00%	4.56%	NA
Japonica Intermediate	241	20.70%	70.10%	0.41%	8.71%	NA
VI/Aromatic	96	90.60%	2.10%	1.04%	6.25%	NA
Intermediate	90	55.60%	27.80%	5.56%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0623074199	A -> G	LOC_Os06g38880.1	downstream_gene_variant ; 4054.0bp to feature; MODIFIER	silent_mutation	Average:78.573; most accessible tissue: Callus, score: 93.333	N	N	N	N
vg0623074199	A -> G	LOC_Os06g38890.1	intron_variant ; MODIFIER	silent_mutation	Average:78.573; most accessible tissue: Callus, score: 93.333	N	N	N	N
vg0623074199	A -> DEL	N	N	silent_mutation	Average:78.573; most accessible tissue: Callus, score: 93.333	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0623074199	1.25E-06	1.25E-06	mr1038	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
vg0623074199	NA	2.67E-08	mr1666	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
vg0623074199	NA	3.80E-06	mr1704	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