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Detailed information for vg0230036530:

Variant ID: vg0230036530 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 30036530
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.03, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

GATCGTCGGCTTGGGTTGATGCAGGTGGCTCCACTTGTGTTGAGGAAGAGGCTCCTTGTTGTGGCTCCCTATGACGTACGTCCCCAAGAGCCAATCTTTT[G/A]
ATTGCTTCGCTCGGATCCTCCTCTTCACCTAACACATGTGAGTCAACTTGCTCTACTTGAGAACCATTAGTTTCATCAAATGTCACATCACGCGCGATCT

Reverse complement sequence

AGATCGCGCGTGATGTGACATTTGATGAAACTAATGGTTCTCAAGTAGAGCAAGTTGACTCACATGTGTTAGGTGAAGAGGAGGATCCGAGCGAAGCAAT[C/T]
AAAAGATTGGCTCTTGGGGACGTACGTCATAGGGAGCCACAACAAGGAGCCTCTTCCTCAACACAAGTGGAGCCACCTGCATCAACCCAAGCCGACGATC

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	67.40%	3.60%	20.44%	8.59%	NA
All Indica	2759	50.10%	5.30%	30.08%	14.50%	NA
All Japonica	1512	99.40%	0.10%	0.46%	0.00%	NA
Aus	269	48.30%	8.20%	43.49%	0.00%	NA
Indica I	595	50.40%	1.80%	32.10%	15.63%	NA
Indica II	465	34.20%	10.30%	43.66%	11.83%	NA
Indica III	913	52.90%	6.50%	24.21%	16.43%	NA
Indica Intermediate	786	56.10%	3.60%	27.35%	12.98%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	98.60%	0.20%	1.19%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	80.00%	1.10%	13.33%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0230036530	G -> A	LOC_Os02g49120.1	synonymous_variant ; p.Ile929Ile; LOW	synonymous_codon	Average:27.18; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg0230036530	G -> DEL	LOC_Os02g49120.1	N	frameshift_variant	Average:27.18; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0230036530	2.26E-07	2.26E-07	mr1575	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