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Detailed information for vg0823525833:

Variant ID: vg0823525833 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 23525833
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACCGCCGTACAACGGCACCTGACAGGAGCGTGTCGTAGGGAAAACGGCGCGAACCGCTTCCTACGAAACCGCGATCTCGGTACCAGTCCCAGGACATAG[T/G]
GTTGGTACCCACGGTGACAAATATGAATCATAGCAATCCTTAAAATAAATAGAGTACTTATTTACCTTAACTTAGGTTGCAGCTCAGACAGCCCGAGAAT

Reverse complement sequence

ATTCTCGGGCTGTCTGAGCTGCAACCTAAGTTAAGGTAAATAAGTACTCTATTTATTTTAAGGATTGCTATGATTCATATTTGTCACCGTGGGTACCAAC[A/C]
CTATGTCCTGGGACTGGTACCGAGATCGCGGTTTCGTAGGAAGCGGTTCGCGCCGTTTTCCCTACGACACGCTCCTGTCAGGTGCCGTTGTACGGCGGTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.10%	1.40%	7.28%	57.26%	NA
All Indica	2759	2.50%	2.30%	10.80%	84.38%	NA
All Japonica	1512	98.30%	0.00%	0.40%	1.32%	NA
Aus	269	4.80%	0.00%	8.55%	86.62%	NA
Indica I	595	3.00%	4.20%	8.24%	84.54%	NA
Indica II	465	2.20%	6.00%	19.78%	72.04%	NA
Indica III	913	1.00%	0.20%	5.26%	93.54%	NA
Indica Intermediate	786	4.10%	1.10%	13.87%	80.92%	NA
Temperate Japonica	767	98.30%	0.00%	0.13%	1.56%	NA
Tropical Japonica	504	99.20%	0.00%	0.60%	0.20%	NA
Japonica Intermediate	241	96.30%	0.00%	0.83%	2.90%	NA
VI/Aromatic	96	4.20%	0.00%	11.46%	84.38%	NA
Intermediate	90	43.30%	1.10%	6.67%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0823525833	T -> G	LOC_Os08g37220-LOC_Os08g37240	intergenic_region ; MODIFIER	silent_mutation	Average:15.961; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0823525833	T -> DEL	N	N	silent_mutation	Average:15.961; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0823525833	4.10E-06	NA	mr1128	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
vg0823525833	7.12E-06	NA	mr1128	Ind_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
vg0823525833	NA	5.54E-06	mr1308	Ind_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
vg0823525833	NA	9.02E-11	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
vg0823525833	NA	2.72E-10	mr1819	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
vg0823525833	NA	1.65E-16	mr1557_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
vg0823525833	NA	1.16E-24	mr1653_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
vg0823525833	NA	2.14E-11	mr1714_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
vg0823525833	NA	6.39E-11	mr1806_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
vg0823525833	NA	2.74E-14	mr1838_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
vg0823525833	NA	5.44E-22	mr1968_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
vg0823525833	NA	3.46E-11	mr1986_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
vg0823525833	NA	4.96E-06	mr1992_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