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Detailed information for vg1100923431:

Variant ID: vg1100923431 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 923431
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGCATTTTGAGAACTTAGCGAATAGTTGATGATCCCTGAGCTTTCCCATTATCAGCCTCAGGTGTTCAGCATGTTCTTCCTCATTCTTGGAGTATATCA[G/A]
GATGTCATCGATGAATACCACGACAAACTGGTCCAGGTATTCCACGAAGATTTTGTTCATTAAGTTCATGAAGAATGCTGGAGCATTGGTGAGTCCGAAG

Reverse complement sequence

CTTCGGACTCACCAATGCTCCAGCATTCTTCATGAACTTAATGAACAAAATCTTCGTGGAATACCTGGACCAGTTTGTCGTGGTATTCATCGATGACATC[C/T]
TGATATACTCCAAGAATGAGGAAGAACATGCTGAACACCTGAGGCTGATAATGGGAAAGCTCAGGGATCATCAACTATTCGCTAAGTTCTCAAAATGCGA

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	89.70%	0.10%	2.18%	8.04%	NA
All Indica	2759	83.40%	0.20%	3.62%	12.83%	NA
All Japonica	1512	98.80%	0.00%	0.07%	1.12%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	78.30%	0.00%	7.06%	14.62%	NA
Indica II	465	86.50%	0.40%	2.15%	10.97%	NA
Indica III	913	86.30%	0.10%	1.10%	12.49%	NA
Indica Intermediate	786	81.90%	0.30%	4.83%	12.98%	NA
Temperate Japonica	767	98.20%	0.00%	0.13%	1.69%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	0.00%	1.11%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1100923431	G -> A	LOC_Os11g02780.1	synonymous_variant ; p.Leu1039Leu; LOW	synonymous_codon	Average:25.713; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1100923431	G -> DEL	LOC_Os11g02780.1	N	frameshift_variant	Average:25.713; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1100923431	3.60E-06	3.59E-06	mr1455	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