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Detailed information for vg0116103237:

Variant ID: vg0116103237 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 16103237
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTCTATCCCTATAGTTCTATTAGCACTAAGCATGGCTAAGCATTAATGAATAAGACATCCCAAGTAATCCCAACCAGTGGTAATAGGGTATAAGACAAC[G/A]
ATATCACAAGAACTAAATGCATTAATAGGTTCTACCCATACACCATAAACCGACAATATTAATATCTAGGCAATACATGCATATATATATATATATATAT

Reverse complement sequence

ATATATATATATATATATATGCATGTATTGCCTAGATATTAATATTGTCGGTTTATGGTGTATGGGTAGAACCTATTAATGCATTTAGTTCTTGTGATAT[C/T]
GTTGTCTTATACCCTATTACCACTGGTTGGGATTACTTGGGATGTCTTATTCATTAATGCTTAGCCATGCTTAGTGCTAATAGAACTATAGGGATAGACA

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	87.80%	10.30%	1.90%	0.00%	NA
All Indica	2759	99.60%	0.30%	0.07%	0.00%	NA
All Japonica	1512	63.30%	31.20%	5.56%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.40%	0.13%	0.00%	NA
Temperate Japonica	767	39.50%	51.90%	8.60%	0.00%	NA
Tropical Japonica	504	96.20%	1.80%	1.98%	0.00%	NA
Japonica Intermediate	241	70.10%	26.60%	3.32%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	90.00%	6.70%	3.33%	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
vg0116103237	G -> A	LOC_Os01g28750.1	upstream_gene_variant ; 1508.0bp to feature; MODIFIER	silent_mutation	Average:38.596; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0116103237	G -> A	LOC_Os01g28744.1	intron_variant ; MODIFIER	silent_mutation	Average:38.596; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0116103237	NA	1.53E-14	Spikelet_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0116103237	NA	9.12E-06	mr1034	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
vg0116103237	NA	5.50E-06	mr1077	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
vg0116103237	NA	9.08E-07	mr1164	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
vg0116103237	NA	3.71E-06	mr1170	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
vg0116103237	NA	9.62E-07	mr1183	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
vg0116103237	NA	2.49E-08	mr1202	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
vg0116103237	NA	9.02E-08	mr1252	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
vg0116103237	4.72E-07	2.14E-06	mr1412	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
vg0116103237	NA	5.06E-09	mr1486	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
vg0116103237	NA	1.38E-07	mr1548	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
vg0116103237	NA	8.50E-07	mr1555	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
vg0116103237	NA	8.64E-08	mr1576	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
vg0116103237	NA	3.87E-06	mr1576	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
vg0116103237	NA	1.54E-07	mr1627	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
vg0116103237	4.87E-06	NA	mr1789	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