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Detailed information for vg1101202802:

Variant ID: vg1101202802 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 1202802
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTCTTTGCACTCCAGAATTGGGCAATAATAGCTTGCAATGGCGGCTCATCATGTCATGAGCATCGCCGCAGCAGCAGTAGCCATGCTTCTCCTGATGGC[G/A]
TCGTCGCCGGCAGTCGCCGGCACGGCGGTGCTCGGCCGGAAGGGCGGCGCCATGACTGACGACGATGTCGTGGGAGGGCAGGCGGCGACAGGGCCGGGGA

Reverse complement sequence

TCCCCGGCCCTGTCGCCGCCTGCCCTCCCACGACATCGTCGTCAGTCATGGCGCCGCCCTTCCGGCCGAGCACCGCCGTGCCGGCGACTGCCGGCGACGA[C/T]
GCCATCAGGAGAAGCATGGCTACTGCTGCTGCGGCGATGCTCATGACATGATGAGCCGCCATTGCAAGCTATTATTGCCCAATTCTGGAGTGCAAAGACT

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	89.60%	4.70%	5.71%	0.00%	NA
All Indica	2759	82.70%	7.90%	9.39%	0.00%	NA
All Japonica	1512	99.50%	0.10%	0.40%	0.00%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	45.40%	24.00%	30.59%	0.00%	NA
Indica II	465	91.40%	3.20%	5.38%	0.00%	NA
Indica III	913	99.50%	0.40%	0.11%	0.00%	NA
Indica Intermediate	786	86.50%	7.00%	6.49%	0.00%	NA
Temperate Japonica	767	99.30%	0.10%	0.52%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1101202802	G -> A	LOC_Os11g03270.1	synonymous_variant ; p.Ala21Ala; LOW	synonymous_codon	Average:64.753; most accessible tissue: Callus, score: 82.626	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1101202802	4.15E-06	NA	mr1642_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