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Detailed information for vg0405180284:

Variant ID: vg0405180284 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5180284
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TTAAAAAAATTCATCGCATATAATGCCGAATTTAACTACATGTTTTTTTCATGTGAAGGCATCAGATGGCGGCGGCGGTCGTCAGCGGTGGGCCATCGGC[G/A]
TTCGAGAGGGCGCACGGGATGCCATTGTTTGAGTACATGGGGACGAACCACCGGTTCAATATGCTGTTCAACCAGGCCATGTCGCAGCAGTCCATGATGG

Reverse complement sequence

CCATCATGGACTGCTGCGACATGGCCTGGTTGAACAGCATATTGAACCGGTGGTTCGTCCCCATGTACTCAAACAATGGCATCCCGTGCGCCCTCTCGAA[C/T]
GCCGATGGCCCACCGCTGACGACCGCCGCCGCCATCTGATGCCTTCACATGAAAAAAACATGTAGTTAAATTCGGCATTATATGCGATGAATTTTTTTAA

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	62.10%	37.40%	0.38%	0.13%	NA
All Indica	2759	40.90%	58.50%	0.43%	0.14%	NA
All Japonica	1512	94.30%	5.50%	0.20%	0.00%	NA
Aus	269	88.10%	11.90%	0.00%	0.00%	NA
Indica I	595	67.60%	31.90%	0.50%	0.00%	NA
Indica II	465	35.70%	64.10%	0.22%	0.00%	NA
Indica III	913	20.70%	79.00%	0.22%	0.11%	NA
Indica Intermediate	786	47.30%	51.50%	0.76%	0.38%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	85.30%	14.30%	0.40%	0.00%	NA
Japonica Intermediate	241	96.70%	2.90%	0.41%	0.00%	NA
VI/Aromatic	96	95.80%	2.10%	1.04%	1.04%	NA
Intermediate	90	56.70%	40.00%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405180284	G -> DEL	LOC_Os04g09654.1	N	frameshift_variant	Average:49.577; most accessible tissue: Callus, score: 68.278	N	N	N	N
vg0405180284	G -> DEL	LOC_Os04g09654.2	N	frameshift_variant	Average:49.577; most accessible tissue: Callus, score: 68.278	N	N	N	N
vg0405180284	G -> A	LOC_Os04g09654.1	synonymous_variant ; p.Ala161Ala; LOW	synonymous_codon	Average:49.577; most accessible tissue: Callus, score: 68.278	N	N	N	N
vg0405180284	G -> A	LOC_Os04g09654.2	synonymous_variant ; p.Ala161Ala; LOW	synonymous_codon	Average:49.577; most accessible tissue: Callus, score: 68.278	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405180284	2.83E-06	7.75E-09	mr1062_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