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Detailed information for vg0802601304:

Variant ID: vg0802601304 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2601304
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCGCATCATCTCTAAGAGAAAAGGGAAACAACTTCCACGTTAGAGTTTCATGTGTCATGCCTACGATGGATAGGCATGAACACACCAGCTCAAAGTCCC[G/A]
AAGATGGAGGTATGGGTTTCCACTAATACCACCAGAGAAGGTTTGCTCTCGAACCATGGCTATAAAGCCAGGACCGATTTCGTAGCCATCTGAAACGATT

Reverse complement sequence

AATCGTTTCAGATGGCTACGAAATCGGTCCTGGCTTTATAGCCATGGTTCGAGAGCAAACCTTCTCTGGTGGTATTAGTGGAAACCCATACCTCCATCTT[C/T]
GGGACTTTGAGCTGGTGTGTTCATGCCTATCCATCGTAGGCATGACACATGAAACTCTAACGTGGAAGTTGTTTCCCTTTTCTCTTAGAGATGATGCGAA

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	94.30%	2.50%	1.21%	1.97%	NA
All Indica	2759	96.00%	0.00%	1.34%	2.68%	NA
All Japonica	1512	91.70%	7.50%	0.73%	0.13%	NA
Aus	269	91.80%	0.00%	2.60%	5.58%	NA
Indica I	595	98.80%	0.00%	0.67%	0.50%	NA
Indica II	465	98.50%	0.00%	0.86%	0.65%	NA
Indica III	913	92.90%	0.00%	1.53%	5.59%	NA
Indica Intermediate	786	95.90%	0.00%	1.91%	2.16%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	77.00%	20.80%	1.98%	0.20%	NA
Japonica Intermediate	241	96.70%	3.30%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	5.60%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0802601304	G -> A	LOC_Os08g05060.1	missense_variant ; p.Arg91Trp; MODERATE	nonsynonymous_codon ; R91W	Average:51.506; most accessible tissue: Minghui63 panicle, score: 70.194	unknown	unknown	DELETERIOUS	0.04
vg0802601304	G -> DEL	LOC_Os08g05060.1	N	frameshift_variant	Average:51.506; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802601304	NA	7.86E-06	mr1073	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
vg0802601304	NA	4.83E-10	mr1217	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
vg0802601304	NA	3.76E-06	mr1830	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
vg0802601304	NA	3.27E-09	mr1845	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