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Detailed information for vg1123883692:

Variant ID: vg1123883692 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23883692
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGCATCATTGAGAGCTGTCGGCCAATAGAAACCTTGACGAAAGGCTTTGCCAACCAAGGTGCGCGAGGCGGAGTGGGCTCCGCATTCGCCTTCATGGAT[G/A]
TCGGCGAGAAGCTCGACGCCTTGTTCCCGAGGAATGCACTTCAGGAGGATTCCATTAGCCGCGCGCCGATAGAGGGTCCCTTCTACCAGCACGTAGCGTT

Reverse complement sequence

AACGCTACGTGCTGGTAGAAGGGACCCTCTATCGGCGCGCGGCTAATGGAATCCTCCTGAAGTGCATTCCTCGGGAACAAGGCGTCGAGCTTCTCGCCGA[C/T]
ATCCATGAAGGCGAATGCGGAGCCCACTCCGCCTCGCGCACCTTGGTTGGCAAAGCCTTTCGTCAAGGTTTCTATTGGCCGACAGCTCTCAATGATGCGG

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	71.30%	0.40%	6.54%	21.79%	NA
All Indica	2759	78.00%	0.70%	5.29%	16.02%	NA
All Japonica	1512	53.50%	0.00%	8.99%	37.50%	NA
Aus	269	89.60%	0.00%	8.18%	2.23%	NA
Indica I	595	56.60%	0.00%	12.10%	31.26%	NA
Indica II	465	67.70%	0.60%	6.45%	25.16%	NA
Indica III	913	95.90%	1.10%	0.66%	2.30%	NA
Indica Intermediate	786	79.50%	0.60%	4.83%	15.01%	NA
Temperate Japonica	767	64.80%	0.00%	5.08%	30.12%	NA
Tropical Japonica	504	44.20%	0.00%	16.47%	39.29%	NA
Japonica Intermediate	241	36.90%	0.00%	5.81%	57.26%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	76.70%	1.10%	5.56%	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
vg1123883692	G -> A	LOC_Os11g40060.1	synonymous_variant ; p.Asp1562Asp; LOW	synonymous_codon	Average:6.556; most accessible tissue: Minghui63 flower, score: 11.139	N	N	N	N
vg1123883692	G -> DEL	LOC_Os11g40060.1	N	frameshift_variant	Average:6.556; most accessible tissue: Minghui63 flower, score: 11.139	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123883692	3.71E-06	3.70E-06	mr1355	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