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Detailed information for vg0727505200:

Variant ID: vg0727505200 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 27505200
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAACCCTCGTCCGCCGTGGTGGATTCACAGGCCAATGGGGAGTTGAATCTGTCAATCTATACTACACATACGCCTTCGAGAAAAACATGGAAGGAGGTGT[A/G]
TTTGCTGCAAAGAGGATCAGCCTCAGCAACTTTGCCATGGATTCTATAAATTCTGACTTGTCCAAGAAACAGCTGTATGGGATCTGGATGATGCACATTT

Reverse complement sequence

AAATGTGCATCATCCAGATCCCATACAGCTGTTTCTTGGACAAGTCAGAATTTATAGAATCCATGGCAAAGTTGCTGAGGCTGATCCTCTTTGCAGCAAA[T/C]
ACACCTCCTTCCATGTTTTTCTCGAAGGCGTATGTGTAGTATAGATTGACAGATTCAACTCCCCATTGGCCTGTGAATCCACCACGGCGGACGAGGGTTC

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	19.50%	0.50%	5.40%	74.61%	NA
All Indica	2759	8.20%	0.30%	5.29%	86.23%	NA
All Japonica	1512	43.70%	0.80%	1.32%	54.23%	NA
Aus	269	1.50%	0.40%	27.14%	71.00%	NA
Indica I	595	11.30%	0.00%	0.67%	88.07%	NA
Indica II	465	6.20%	0.20%	1.08%	92.47%	NA
Indica III	913	8.50%	0.70%	10.95%	79.85%	NA
Indica Intermediate	786	6.50%	0.30%	4.71%	88.55%	NA
Temperate Japonica	767	66.80%	0.30%	0.65%	32.33%	NA
Tropical Japonica	504	15.10%	1.60%	2.58%	80.75%	NA
Japonica Intermediate	241	29.90%	0.80%	0.83%	68.46%	NA
VI/Aromatic	96	4.20%	0.00%	12.50%	83.33%	NA
Intermediate	90	33.30%	0.00%	4.44%	62.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0727505200	A -> DEL	LOC_Os07g46080.1	N	frameshift_variant	Average:10.519; most accessible tissue: Callus, score: 45.11	N	N	N	N
vg0727505200	A -> G	LOC_Os07g46080.1	synonymous_variant ; p.Val300Val; LOW	synonymous_codon	Average:10.519; most accessible tissue: Callus, score: 45.11	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0727505200	NA	6.39E-10	Heading_date	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
vg0727505200	NA	1.78E-09	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
vg0727505200	NA	1.57E-13	mr1002	Jap_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
vg0727505200	NA	2.65E-06	mr1187	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
vg0727505200	NA	9.60E-12	mr1578	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
vg0727505200	NA	4.41E-07	mr1756	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
vg0727505200	NA	2.34E-08	mr1915	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
vg0727505200	NA	2.26E-06	mr1952	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
vg0727505200	NA	3.79E-14	mr1002_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
vg0727505200	NA	7.56E-06	mr1186_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
vg0727505200	NA	3.24E-06	mr1330_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
vg0727505200	NA	9.40E-06	mr1616_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
vg0727505200	NA	6.90E-07	mr1671_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
vg0727505200	NA	4.98E-07	mr1819_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
vg0727505200	NA	5.56E-09	mr1851_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
vg0727505200	NA	2.78E-06	mr1966_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