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Detailed information for vg0124727516:

Variant ID: vg0124727516 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24727516
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAACTAACGGTCAACAAACGGAATGTGTATGAAAGGGATCAAAACCAAAATTCAAGGGCATATAAGGGAGTGGACAAAACTCGGGAGCATAGAAGGGATT[A/G]
GCTAAACTTTCAGAGGTATAGAAGGAATTTTCTCTATATACAGAGAGGGAGGGTGTGTCCTCCCGGTATTGTTTCAGAGAGAGTTGAGTTGAGAGAATAG

Reverse complement sequence

CTATTCTCTCAACTCAACTCTCTCTGAAACAATACCGGGAGGACACACCCTCCCTCTCTGTATATAGAGAAAATTCCTTCTATACCTCTGAAAGTTTAGC[T/C]
AATCCCTTCTATGCTCCCGAGTTTTGTCCACTCCCTTATATGCCCTTGAATTTTGGTTTTGATCCCTTTCATACACATTCCGTTTGTTGACCGTTAGTTG

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	78.40%	21.20%	0.11%	0.34%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	38.20%	60.40%	0.33%	1.06%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	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	99.50%	0.50%	0.00%	0.00%	NA
Temperate Japonica	767	19.70%	80.20%	0.13%	0.00%	NA
Tropical Japonica	504	71.00%	27.60%	0.20%	1.19%	NA
Japonica Intermediate	241	28.20%	66.40%	1.24%	4.15%	NA
VI/Aromatic	96	41.70%	58.30%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0124727516	A -> G	LOC_Os01g43274-LOC_Os01g43280	intergenic_region ; MODIFIER	silent_mutation	Average:33.813; most accessible tissue: Callus, score: 58.32	N	N	N	N
vg0124727516	A -> DEL	N	N	silent_mutation	Average:33.813; most accessible tissue: Callus, score: 58.32	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124727516	NA	5.29E-07	mr1002	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
vg0124727516	NA	2.27E-06	mr1002	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
vg0124727516	7.24E-07	NA	mr1388	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
vg0124727516	NA	2.23E-07	mr1388	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
vg0124727516	8.35E-06	NA	mr1757	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
vg0124727516	9.54E-08	NA	mr1238_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
vg0124727516	4.50E-07	NA	mr1484_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
vg0124727516	NA	5.60E-08	mr1568_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
vg0124727516	1.35E-06	NA	mr1757_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
vg0124727516	NA	1.80E-06	mr1757_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
vg0124727516	5.04E-07	NA	mr1841_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
vg0124727516	4.74E-06	NA	mr1900_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
vg0124727516	4.09E-07	8.55E-19	mr1945_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