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Detailed information for vg1127472745:

Variant ID: vg1127472745 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27472745
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTCATAAAAATAAATAATAATTCCAAATTTTCTTTGAATAAGACAACTGGTCAAACAGTGTAAGAAAAATGTCAAAATCCTTTATATTAGAGTACGGAG[G/A]
GAGTAGTAAGCAATTAAAAGAGTTAAATTTTGCGTACGCACGCACCTCCACTGCCTTCTTCAAGGCAGGTCTGAAATCGGTATTGCCGCTGGCCTTGAGC

Reverse complement sequence

GCTCAAGGCCAGCGGCAATACCGATTTCAGACCTGCCTTGAAGAAGGCAGTGGAGGTGCGTGCGTACGCAAAATTTAACTCTTTTAATTGCTTACTACTC[C/T]
CTCCGTACTCTAATATAAAGGATTTTGACATTTTTCTTACACTGTTTGACCAGTTGTCTTATTCAAAGAAAATTTGGAATTATTATTTATTTTTATGACT

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	83.10%	1.50%	0.38%	15.09%	NA
All Indica	2759	86.40%	0.30%	0.33%	13.01%	NA
All Japonica	1512	77.30%	3.60%	0.46%	18.65%	NA
Aus	269	78.80%	2.60%	0.74%	17.84%	NA
Indica I	595	95.60%	0.00%	0.00%	4.37%	NA
Indica II	465	93.80%	1.30%	0.22%	4.73%	NA
Indica III	913	80.50%	0.00%	0.33%	19.17%	NA
Indica Intermediate	786	81.90%	0.10%	0.64%	17.30%	NA
Temperate Japonica	767	86.20%	1.40%	0.52%	11.86%	NA
Tropical Japonica	504	62.30%	5.00%	0.40%	32.34%	NA
Japonica Intermediate	241	80.50%	7.50%	0.41%	11.62%	NA
VI/Aromatic	96	90.60%	0.00%	0.00%	9.38%	NA
Intermediate	90	81.10%	2.20%	0.00%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127472745	G -> A	LOC_Os11g45390.1	intron_variant ; MODIFIER	silent_mutation	Average:66.869; most accessible tissue: Minghui63 root, score: 83.538	N	N	N	N
vg1127472745	G -> DEL	N	N	silent_mutation	Average:66.869; most accessible tissue: Minghui63 root, score: 83.538	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127472745	1.51E-08	1.96E-06	mr1719	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
vg1127472745	NA	5.13E-06	mr1620_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
vg1127472745	NA	7.83E-06	mr1850_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