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Detailed information for vg0823460770:

Variant ID: vg0823460770 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 23460770
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGATAAACAAGCAGTTACCTTTTCTAGATGCTCTTATCCAATCCTTGGTACAAACTAGAACTGCGAAAAGGACCAACAACAAGACCACCAGCACTAAAC[G/A]
CTGACTCTGAAGCAACGGTAGATATTTGAACAGCCATTACATCACGCGCGAGTGTTGAGAGGATAGGAAAGGTCATTTGGTTGCTCTTCCACCATGCCAG

Reverse complement sequence

CTGGCATGGTGGAAGAGCAACCAAATGACCTTTCCTATCCTCTCAACACTCGCGCGTGATGTAATGGCTGTTCAAATATCTACCGTTGCTTCAGAGTCAG[C/T]
GTTTAGTGCTGGTGGTCTTGTTGTTGGTCCTTTTCGCAGTTCTAGTTTGTACCAAGGATTGGATAAGAGCATCTAGAAAAGGTAACTGCTTGTTTATCTT

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	31.00%	3.00%	21.01%	44.92%	NA
All Indica	2759	2.80%	0.10%	25.77%	71.37%	NA
All Japonica	1512	87.70%	9.10%	2.18%	1.06%	NA
Aus	269	8.20%	0.00%	64.68%	27.14%	NA
Indica I	595	3.70%	0.00%	10.76%	85.55%	NA
Indica II	465	2.20%	0.00%	27.31%	70.54%	NA
Indica III	913	1.60%	0.10%	30.78%	67.47%	NA
Indica Intermediate	786	3.80%	0.10%	30.41%	65.65%	NA
Temperate Japonica	767	97.40%	0.10%	1.30%	1.17%	NA
Tropical Japonica	504	71.80%	25.00%	2.78%	0.40%	NA
Japonica Intermediate	241	90.00%	4.10%	3.73%	2.07%	NA
VI/Aromatic	96	5.20%	0.00%	57.29%	37.50%	NA
Intermediate	90	40.00%	5.60%	22.22%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0823460770	G -> A	LOC_Os08g37130.1	upstream_gene_variant ; 3163.0bp to feature; MODIFIER	silent_mutation	Average:12.933; most accessible tissue: Minghui63 young leaf, score: 27.355	N	N	N	N
vg0823460770	G -> A	LOC_Os08g37120.1	intron_variant ; MODIFIER	silent_mutation	Average:12.933; most accessible tissue: Minghui63 young leaf, score: 27.355	N	N	N	N
vg0823460770	G -> DEL	N	N	silent_mutation	Average:12.933; most accessible tissue: Minghui63 young leaf, score: 27.355	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0823460770	8.89E-07	NA	mr1301_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
vg0823460770	1.05E-06	NA	mr1410_2	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