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Detailed information for vg0615551230:

Variant ID: vg0615551230 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 15551230
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATGAATACCGAATCCTTGGAAACAGTCTTGACGATAAGAACGTATTCGATGTGAGCAAAATAATGGGTGTCGAATCCTTGGAAACAGTCTTGACGACAC[G/A]
GACGTACCCGGAATAAAAAGAGAAAAAAAATATGAGCAAAAAGGCTCAAGATAAGAAAAGTCCAAAAAATTCTCTTGGTTATTTTGTGCTCAAGGTTATT

Reverse complement sequence

AATAACCTTGAGCACAAAATAACCAAGAGAATTTTTTGGACTTTTCTTATCTTGAGCCTTTTTGCTCATATTTTTTTTCTCTTTTTATTCCGGGTACGTC[C/T]
GTGTCGTCAAGACTGTTTCCAAGGATTCGACACCCATTATTTTGCTCACATCGAATACGTTCTTATCGTCAAGACTGTTTCCAAGGATTCGGTATTCATT

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	67.00%	33.00%	0.02%	0.00%	NA
All Indica	2759	97.80%	2.20%	0.00%	0.00%	NA
All Japonica	1512	9.10%	90.90%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	97.30%	2.70%	0.00%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	95.70%	4.30%	0.00%	0.00%	NA
Temperate Japonica	767	3.80%	96.20%	0.00%	0.00%	NA
Tropical Japonica	504	17.90%	82.10%	0.00%	0.00%	NA
Japonica Intermediate	241	7.50%	92.50%	0.00%	0.00%	NA
VI/Aromatic	96	15.60%	83.30%	1.04%	0.00%	NA
Intermediate	90	56.70%	43.30%	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
vg0615551230	G -> A	LOC_Os06g27460.1	downstream_gene_variant ; 457.0bp to feature; MODIFIER	silent_mutation	Average:24.294; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0615551230	G -> A	LOC_Os06g27470.1	downstream_gene_variant ; 1938.0bp to feature; MODIFIER	silent_mutation	Average:24.294; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0615551230	G -> A	LOC_Os06g27460-LOC_Os06g27470	intergenic_region ; MODIFIER	silent_mutation	Average:24.294; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0615551230	NA	6.89E-19	Yield	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
vg0615551230	NA	4.02E-23	mr1020	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
vg0615551230	NA	3.45E-20	mr1021	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
vg0615551230	NA	3.12E-14	mr1032	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
vg0615551230	4.11E-10	5.86E-79	mr1033	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
vg0615551230	NA	2.04E-16	mr1165	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
vg0615551230	NA	6.25E-40	mr1176	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
vg0615551230	NA	2.45E-18	mr1242	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
vg0615551230	NA	2.32E-06	mr1278	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
vg0615551230	NA	1.48E-20	mr1477	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
vg0615551230	NA	6.05E-15	mr1478	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
vg0615551230	NA	4.11E-75	mr1536	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
vg0615551230	NA	9.09E-11	mr1553	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
vg0615551230	NA	1.80E-21	mr1971	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
vg0615551230	NA	1.04E-07	mr1979	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
vg0615551230	1.78E-10	9.23E-104	mr1033_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
vg0615551230	NA	2.59E-96	mr1536_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