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Detailed information for vg1110033720:

Variant ID: vg1110033720 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10033720
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTCACAGGTGAGGATGCTAGAATAACAATGGAGCATATCGGTCAATTTATTGAACAATGTGGTAAGGCCGATAGTGATGATTTGCTTAAGTTAAAGTT[G/A]
TTTCCTCTTTCTTTGTCAAACTTTGCATCTACATGGTATAGTTTACTTGCTCCCAATTCAATTTCTACATGGTCGCAAATGGAGCATGAATTTCATGATT

Reverse complement sequence

AATCATGAAATTCATGCTCCATTTGCGACCATGTAGAAATTGAATTGGGAGCAAGTAAACTATACCATGTAGATGCAAAGTTTGACAAAGAAAGAGGAAA[C/T]
AACTTTAACTTAAGCAAATCATCACTATCGGCCTTACCACATTGTTCAATAAATTGACCGATATGCTCCATTGTTATTCTAGCATCCTCACCTGTGAATT

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	62.70%	0.10%	7.66%	29.50%	NA
All Indica	2759	50.20%	0.20%	10.91%	38.71%	NA
All Japonica	1512	86.70%	0.00%	1.46%	11.84%	NA
Aus	269	43.10%	0.40%	13.01%	43.49%	NA
Indica I	595	60.50%	0.20%	8.07%	31.26%	NA
Indica II	465	49.50%	0.00%	9.68%	40.86%	NA
Indica III	913	40.20%	0.00%	13.36%	46.44%	NA
Indica Intermediate	786	54.50%	0.50%	10.94%	34.10%	NA
Temperate Japonica	767	79.90%	0.00%	2.35%	17.73%	NA
Tropical Japonica	504	97.20%	0.00%	0.20%	2.58%	NA
Japonica Intermediate	241	86.30%	0.00%	1.24%	12.45%	NA
VI/Aromatic	96	91.70%	0.00%	0.00%	8.33%	NA
Intermediate	90	71.10%	0.00%	4.44%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110033720	G -> A	LOC_Os11g17890.1	synonymous_variant ; p.Leu490Leu; LOW	synonymous_codon	Average:10.643; most accessible tissue: Minghui63 young leaf, score: 15.967	N	N	N	N
vg1110033720	G -> DEL	LOC_Os11g17890.1	N	frameshift_variant	Average:10.643; most accessible tissue: Minghui63 young leaf, score: 15.967	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110033720	NA	5.52E-08	mr1830_2	Ind_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
vg1110033720	9.85E-07	8.10E-18	mr1846_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
vg1110033720	1.20E-06	3.45E-14	mr1846_2	Ind_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