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Detailed information for vg0715474043:

Variant ID: vg0715474043 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15474043
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATGGGTTTTGATAACTAAACCGGCTAGCGGAGCCGATTTCTAGATAACTACCCGTCTCGTGGGCAAAACGGAAGGTTTTTAGGACAAACCTACAAAGAG[G/A]
TGTTGCACTCTCGCTGCGGCGGCGGACGGTTTACGGCGCAAATCGACAAAGATGGACAAATTAAGAGAAAACTAAAAGCAATATGAAAAGAACGATTCGA

Reverse complement sequence

TCGAATCGTTCTTTTCATATTGCTTTTAGTTTTCTCTTAATTTGTCCATCTTTGTCGATTTGCGCCGTAAACCGTCCGCCGCCGCAGCGAGAGTGCAACA[C/T]
CTCTTTGTAGGTTTGTCCTAAAAACCTTCCGTTTTGCCCACGAGACGGGTAGTTATCTAGAAATCGGCTCCGCTAGCCGGTTTAGTTATCAAAACCCATC

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	19.10%	0.20%	20.84%	59.90%	NA
All Indica	2759	9.20%	0.20%	28.42%	62.20%	NA
All Japonica	1512	41.00%	0.00%	3.44%	55.56%	NA
Aus	269	2.20%	1.10%	42.38%	54.28%	NA
Indica I	595	15.60%	0.00%	7.06%	77.31%	NA
Indica II	465	6.50%	0.00%	34.41%	59.14%	NA
Indica III	913	3.20%	0.40%	34.94%	61.45%	NA
Indica Intermediate	786	13.00%	0.10%	33.46%	53.44%	NA
Temperate Japonica	767	71.80%	0.00%	2.35%	25.81%	NA
Tropical Japonica	504	3.20%	0.00%	5.16%	91.67%	NA
Japonica Intermediate	241	22.00%	0.00%	3.32%	74.69%	NA
VI/Aromatic	96	2.10%	0.00%	11.46%	86.46%	NA
Intermediate	90	22.20%	0.00%	26.67%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715474043	G -> DEL	N	N	silent_mutation	Average:16.223; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0715474043	G -> A	LOC_Os07g26780.1	upstream_gene_variant ; 270.0bp to feature; MODIFIER	silent_mutation	Average:16.223; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0715474043	G -> A	LOC_Os07g26780-LOC_Os07g26790	intergenic_region ; MODIFIER	silent_mutation	Average:16.223; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715474043	NA	3.50E-06	mr1682	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
vg0715474043	NA	2.44E-08	mr1153_2	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
vg0715474043	NA	4.22E-06	mr1169_2	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
vg0715474043	NA	2.44E-06	mr1262_2	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
vg0715474043	NA	6.86E-10	mr1659_2	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