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Detailed information for vg0211327855:

Variant ID: vg0211327855 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 11327855
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAATTTGGCCGAGCGGTTCCGGAAAGCCGATGAGGAGAAGCGGCAGGGCCGACGAGAGGGCAAAGCCCCCACGACCTCAGCCGATGACCAGCGAGGGGAG[G/A]
CCAAGAAGAAGGCCCCCGCCGATGATGGCGATGACAGTGAGGATCTGGAGTTCCAGATACCTCAGGGAACTGTCGCCACGCTCGACGAGAGGGCTTGCGC

Reverse complement sequence

GCGCAAGCCCTCTCGTCGAGCGTGGCGACAGTTCCCTGAGGTATCTGGAACTCCAGATCCTCACTGTCATCGCCATCATCGGCGGGGGCCTTCTTCTTGG[C/T]
CTCCCCTCGCTGGTCATCGGCTGAGGTCGTGGGGGCTTTGCCCTCTCGTCGGCCCTGCCGCTTCTCCTCATCGGCTTTCCGGAACCGCTCGGCCAAATTC

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	75.10%	1.50%	9.97%	13.46%	NA
All Indica	2759	59.90%	2.20%	16.20%	21.64%	NA
All Japonica	1512	99.10%	0.00%	0.07%	0.86%	NA
Aus	269	88.10%	2.60%	5.95%	3.35%	NA
Indica I	595	48.40%	1.00%	24.20%	26.39%	NA
Indica II	465	43.20%	3.70%	23.23%	29.89%	NA
Indica III	913	74.90%	3.00%	8.65%	13.47%	NA
Indica Intermediate	786	61.10%	1.50%	14.76%	22.65%	NA
Temperate Japonica	767	99.20%	0.00%	0.00%	0.78%	NA
Tropical Japonica	504	98.60%	0.00%	0.00%	1.39%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	73.30%	1.10%	7.78%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0211327855	G -> A	LOC_Os02g19390.1	missense_variant ; p.Ala227Thr; MODERATE	nonsynonymous_codon ; A227T	Average:21.889; most accessible tissue: Callus, score: 32.088	possibly damaging	1.571	DELETERIOUS	0.01
vg0211327855	G -> DEL	LOC_Os02g19390.1	N	frameshift_variant	Average:21.889; most accessible tissue: Callus, score: 32.088	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0211327855	1.94E-06	2.85E-06	mr1482	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
vg0211327855	5.15E-08	5.15E-08	mr1335_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