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Detailed information for vg0624535916:

Variant ID: vg0624535916 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 24535916
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATCATAAAGAGCTCTGCTATAAATACGATAAATATCTTACTATTAGTGTACGGTGCCTTCTAATCTCTAATACATGCAACAAATATAGGGTCCACAAT[G/A]
TTTCCATGGCCAATCAATTATCATGCATGACACTAGATCGTACCAAAATCGTAACAAGTTTATCTTACGTACATCAATTTCCTATCATAAAACCGACCGG

Reverse complement sequence

CCGGTCGGTTTTATGATAGGAAATTGATGTACGTAAGATAAACTTGTTACGATTTTGGTACGATCTAGTGTCATGCATGATAATTGATTGGCCATGGAAA[C/T]
ATTGTGGACCCTATATTTGTTGCATGTATTAGAGATTAGAAGGCACCGTACACTAATAGTAAGATATTTATCGTATTTATAGCAGAGCTCTTTATGATAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.60%	30.00%	0.32%	0.00%	NA
All Indica	2759	98.20%	1.80%	0.04%	0.00%	NA
All Japonica	1512	16.80%	82.60%	0.60%	0.00%	NA
Aus	269	96.30%	3.70%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	97.60%	2.40%	0.00%	0.00%	NA
Indica III	913	98.70%	1.30%	0.00%	0.00%	NA
Indica Intermediate	786	96.80%	3.10%	0.13%	0.00%	NA
Temperate Japonica	767	2.30%	97.50%	0.13%	0.00%	NA
Tropical Japonica	504	43.50%	55.40%	1.19%	0.00%	NA
Japonica Intermediate	241	7.10%	92.10%	0.83%	0.00%	NA
VI/Aromatic	96	15.60%	83.30%	1.04%	0.00%	NA
Intermediate	90	60.00%	35.60%	4.44%	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
vg0624535916	G -> A	LOC_Os06g41070.1	upstream_gene_variant ; 2118.0bp to feature; MODIFIER	silent_mutation	Average:53.114; most accessible tissue: Zhenshan97 root, score: 84.358	N	N	N	N
vg0624535916	G -> A	LOC_Os06g41070-LOC_Os06g41090	intergenic_region ; MODIFIER	silent_mutation	Average:53.114; most accessible tissue: Zhenshan97 root, score: 84.358	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0624535916	NA	7.46E-06	mr1082	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
vg0624535916	NA	1.17E-17	mr1133	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
vg0624535916	NA	5.41E-07	mr1190	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
vg0624535916	NA	9.83E-19	mr1422	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
vg0624535916	NA	1.33E-07	mr1439	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
vg0624535916	NA	4.92E-07	mr1551	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
vg0624535916	NA	8.11E-21	mr1698	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
vg0624535916	NA	4.79E-06	mr1925	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
vg0624535916	NA	1.09E-24	mr1077_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
vg0624535916	NA	2.44E-12	mr1216_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
vg0624535916	7.22E-09	5.61E-08	mr1498_2	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
vg0624535916	1.52E-06	2.70E-08	mr1498_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
vg0624535916	2.32E-06	5.01E-07	mr1925_2	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