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Detailed information for vg0405141588:

Variant ID: vg0405141588 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5141588
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCTGCTCGATCGGGCGGCGAGCCGGCGAGCGGCGGTGGCAGTGGATGATGCCTGACGATGGGCGACAACCTTGATCCAATAGCGAGAGCAGTCAACGCC[G/A]
GACAACGACCTGCATCCAACAGCGACGGCGATAGACGCCGGGTGGCAGCCGATGACGGGAGGGTGAGCAGCGACCCACGGATCGGCGACGCTCCCTGAGG

Reverse complement sequence

CCTCAGGGAGCGTCGCCGATCCGTGGGTCGCTGCTCACCCTCCCGTCATCGGCTGCCACCCGGCGTCTATCGCCGTCGCTGTTGGATGCAGGTCGTTGTC[C/T]
GGCGTTGACTGCTCTCGCTATTGGATCAAGGTTGTCGCCCATCGTCAGGCATCATCCACTGCCACCGCCGCTCGCCGGCTCGCCGCCCGATCGAGCAGGC

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	88.00%	9.40%	0.25%	2.35%	NA
All Indica	2759	92.60%	5.10%	0.29%	1.96%	NA
All Japonica	1512	76.40%	19.80%	0.26%	3.57%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	95.80%	3.50%	0.00%	0.67%	NA
Indica II	465	92.30%	1.90%	0.22%	5.59%	NA
Indica III	913	92.40%	6.90%	0.33%	0.33%	NA
Indica Intermediate	786	90.70%	6.10%	0.51%	2.67%	NA
Temperate Japonica	767	63.60%	36.40%	0.00%	0.00%	NA
Tropical Japonica	504	86.30%	2.20%	0.79%	10.71%	NA
Japonica Intermediate	241	96.30%	3.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	6.70%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405141588	G -> DEL	N	N	silent_mutation	Average:29.551; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0405141588	G -> A	LOC_Os04g09580.1	5_prime_UTR_premature_start_codon_gain_variant ; LOW	silent_mutation	Average:29.551; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0405141588	G -> A	LOC_Os04g09580.1	5_prime_UTR_variant ; 932.0bp to feature; MODIFIER	silent_mutation	Average:29.551; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405141588	3.28E-07	NA	mr1062	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405141588	NA	1.35E-08	mr1062	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405141588	4.43E-06	2.24E-06	mr1525	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0405141588	3.01E-07	NA	mr1631_2	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
vg0405141588	NA	3.18E-06	mr1631_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251