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Detailed information for vg0707567583:

Variant ID: vg0707567583 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 7567583
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.77, G: 0.23, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

ACCTGAATAAAGCATGTCCGAAAGACGACTTCCCCTTGCCGCGAATCGACCAACTCTGGGGGCGAAGAGGGGCGCGAAGTATCGCTCGAACTCTTAGAAG[G/A]
AGTAAGGGTCGAAGCGCTCGAGCACATGCACAAGTACGCCACAAGCACTTCGGCAACTTACAACAAAAAAGTTCGACCCACGCAGCTGATGCCTGGTCAT

Reverse complement sequence

ATGACCAGGCATCAGCTGCGTGGGTCGAACTTTTTTGTTGTAAGTTGCCGAAGTGCTTGTGGCGTACTTGTGCATGTGCTCGAGCGCTTCGACCCTTACT[C/T]
CTTCTAAGAGTTCGAGCGATACTTCGCGCCCCTCTTCGCCCCCAGAGTTGGTCGATTCGCGGCAAGGGGAAGTCGTCTTTCGGACATGCTTTATTCAGGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.50%	34.90%	1.38%	4.25%	NA
All Indica	2759	93.30%	6.20%	0.25%	0.25%	NA
All Japonica	1512	5.30%	79.70%	2.45%	12.57%	NA
Aus	269	33.50%	59.10%	7.43%	0.00%	NA
Indica I	595	98.00%	2.00%	0.00%	0.00%	NA
Indica II	465	91.20%	7.10%	0.65%	1.08%	NA
Indica III	913	96.80%	2.60%	0.44%	0.11%	NA
Indica Intermediate	786	87.00%	12.80%	0.00%	0.13%	NA
Temperate Japonica	767	1.20%	95.80%	0.39%	2.61%	NA
Tropical Japonica	504	12.10%	68.30%	6.15%	13.49%	NA
Japonica Intermediate	241	4.10%	52.30%	1.24%	42.32%	NA
VI/Aromatic	96	24.00%	76.00%	0.00%	0.00%	NA
Intermediate	90	47.80%	46.70%	1.11%	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
vg0707567583	G -> DEL	LOC_Os07g13190.1	N	frameshift_variant	Average:39.022; most accessible tissue: Minghui63 young leaf, score: 74.007	N	N	N	N
vg0707567583	G -> A	LOC_Os07g13190.1	synonymous_variant ; p.Arg896Arg; LOW	synonymous_codon	Average:39.022; most accessible tissue: Minghui63 young leaf, score: 74.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0707567583	NA	1.17E-12	mr1056	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
vg0707567583	NA	5.51E-10	mr1195	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
vg0707567583	NA	6.81E-12	mr1329	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
vg0707567583	NA	6.48E-13	mr1362	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
vg0707567583	NA	2.12E-10	mr1379	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
vg0707567583	NA	1.10E-07	mr1559	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
vg0707567583	NA	2.92E-10	mr1581	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
vg0707567583	NA	3.28E-07	mr1716	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
vg0707567583	NA	6.55E-08	mr1804	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
vg0707567583	NA	9.80E-14	mr1982	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
vg0707567583	NA	5.79E-09	mr1379_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
vg0707567583	NA	5.38E-17	mr1457_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
vg0707567583	2.30E-06	NA	mr1543_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
vg0707567583	NA	2.19E-06	mr1559_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
vg0707567583	NA	7.53E-08	mr1690_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