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Detailed information for vg0806548377:

Variant ID: vg0806548377 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 6548377
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCAATTCTTTTTGATCTAGATTCTCGCGGCCCACTGCTCGACCGAGCGAACCATGTGGGCTCATATTGACGGCTTCAAGAACCATCTTCGAGCCAAGGAC[A/G]
ATGAACTGGGTCGCAAGAGCTTGGAGATGGAGGGCCTCGCCAACACCCTCAAAGAGGCGAAGGCTGAGAACAAGTGGCTCCAAGCTGAGCTGGAGAAGGG

Reverse complement sequence

CCCTTCTCCAGCTCAGCTTGGAGCCACTTGTTCTCAGCCTTCGCCTCTTTGAGGGTGTTGGCGAGGCCCTCCATCTCCAAGCTCTTGCGACCCAGTTCAT[T/C]
GTCCTTGGCTCGAAGATGGTTCTTGAAGCCGTCAATATGAGCCCACATGGTTCGCTCGGTCGAGCAGTGGGCCGCGAGAATCTAGATCAAAAAGAATTGA

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	32.70%	13.30%	7.22%	46.72%	NA
All Indica	2759	14.00%	9.80%	6.20%	70.03%	NA
All Japonica	1512	73.70%	23.30%	0.53%	2.38%	NA
Aus	269	1.90%	0.70%	48.33%	49.07%	NA
Indica I	595	30.80%	6.10%	2.86%	60.34%	NA
Indica II	465	9.50%	2.80%	4.52%	83.23%	NA
Indica III	913	5.00%	13.60%	7.45%	73.93%	NA
Indica Intermediate	786	14.20%	12.50%	8.27%	65.01%	NA
Temperate Japonica	767	55.00%	42.20%	0.78%	1.96%	NA
Tropical Japonica	504	96.20%	0.80%	0.40%	2.58%	NA
Japonica Intermediate	241	86.30%	10.40%	0.00%	3.32%	NA
VI/Aromatic	96	3.10%	1.00%	27.08%	68.75%	NA
Intermediate	90	43.30%	3.30%	6.67%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0806548377	A -> G	LOC_Os08g11130.1	missense_variant ; p.Asn532Asp; MODERATE	nonsynonymous_codon	Average:10.551; most accessible tissue: Callus, score: 28.358	possibly damaging	-1.653	TOLERATED	1.00
vg0806548377	A -> DEL	LOC_Os08g11130.1	N	frameshift_variant	Average:10.551; most accessible tissue: Callus, score: 28.358	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0806548377	NA	4.40E-17	mr1035	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
vg0806548377	NA	8.61E-07	mr1035	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
vg0806548377	NA	1.53E-13	mr1149	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
vg0806548377	NA	3.21E-08	mr1162	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
vg0806548377	3.33E-06	8.17E-07	mr1415	Ind_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
vg0806548377	NA	1.31E-08	mr1510	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
vg0806548377	3.33E-06	8.17E-07	mr1567	Ind_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
vg0806548377	NA	4.99E-13	mr1626	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
vg0806548377	NA	4.94E-10	mr1630	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
vg0806548377	NA	5.50E-10	mr1648	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
vg0806548377	NA	2.11E-17	mr1062_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
vg0806548377	NA	7.35E-07	mr1062_2	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
vg0806548377	NA	6.52E-06	mr1080_2	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