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Detailed information for vg0809622371:

Variant ID: vg0809622371 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9622371
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGTGGACCGTTTCCAGTAACATCTGTTGATGGATATGATTCATTCATTACCTTCACAGATGATTTCTCCCGTTATGGATATGTTTTCCCCATTAAAGAT[A/C]
GATCTGAATCACTCGATAAGTTTAAAATATTCAAAGCTGAGGTTGAAAATCAGCACAATGCAAAAATTAAGGTAGTGAGATCAGATCGAGGAGGAGAATA

Reverse complement sequence

TATTCTCCTCCTCGATCTGATCTCACTACCTTAATTTTTGCATTGTGCTGATTTTCAACCTCAGCTTTGAATATTTTAAACTTATCGAGTGATTCAGATC[T/G]
ATCTTTAATGGGGAAAACATATCCATAACGGGAGAAATCATCTGTGAAGGTAATGAATGAATCATATCCATCAACAGATGTTACTGGAAACGGTCCACAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.30%	0.20%	0.78%	0.72%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.00%	NA
All Japonica	1512	95.20%	0.40%	2.18%	2.18%	NA
Aus	269	97.80%	1.10%	1.12%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	91.00%	0.70%	4.17%	4.17%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0809622371	A -> C	LOC_Os08g15830.1	synonymous_variant ; p.Arg623Arg; LOW	synonymous_codon	Average:18.598; most accessible tissue: Zhenshan97 flag leaf, score: 39.979	N	N	N	N
vg0809622371	A -> DEL	LOC_Os08g15830.1	N	frameshift_variant	Average:18.598; most accessible tissue: Zhenshan97 flag leaf, score: 39.979	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809622371	1.41E-06	1.72E-10	mr1062	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
vg0809622371	3.73E-07	3.73E-07	mr1525	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