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Detailed information for vg0421205174:

Variant ID: vg0421205174 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21205174
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTCGTGTTGTTTATTTGGATATCCATGATTGTTTCATGGTTATGGCTTCTAGATGGATACTATACGTATGTAATACTGTTCTTTGCTAACAATGAGTC[G/A]
AGTTGGAGATAGCTTGGTCTCGAAATATGGTTTCTTTGTTTGTTTCATGTGTAGGTGACTCGATGCCTCGGGAGAGTATTTGCGGTGATGGACCGGGAGT

Reverse complement sequence

ACTCCCGGTCCATCACCGCAAATACTCTCCCGAGGCATCGAGTCACCTACACATGAAACAAACAAAGAAACCATATTTCGAGACCAAGCTATCTCCAACT[C/T]
GACTCATTGTTAGCAAAGAACAGTATTACATACGTATAGTATCCATCTAGAAGCCATAACCATGAAACAATCATGGATATCCAAATAAACAACACGAAAC

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	64.30%	0.10%	2.62%	32.88%	NA
All Indica	2759	48.60%	0.20%	3.91%	47.34%	NA
All Japonica	1512	98.50%	0.00%	0.13%	1.39%	NA
Aus	269	32.30%	0.00%	3.35%	64.31%	NA
Indica I	595	48.70%	0.00%	1.34%	49.92%	NA
Indica II	465	39.80%	0.20%	2.37%	57.63%	NA
Indica III	913	51.80%	0.10%	6.46%	41.62%	NA
Indica Intermediate	786	49.90%	0.40%	3.82%	45.93%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	95.60%	0.00%	0.40%	3.97%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	55.20%	0.00%	3.12%	41.67%	NA
Intermediate	90	80.00%	2.20%	2.22%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0421205174	G -> DEL	N	N	silent_mutation	Average:8.641; most accessible tissue: Callus, score: 18.805	N	N	N	N
vg0421205174	G -> A	LOC_Os04g34900.1	upstream_gene_variant ; 1852.0bp to feature; MODIFIER	silent_mutation	Average:8.641; most accessible tissue: Callus, score: 18.805	N	N	N	N
vg0421205174	G -> A	LOC_Os04g34890-LOC_Os04g34900	intergenic_region ; MODIFIER	silent_mutation	Average:8.641; most accessible tissue: Callus, score: 18.805	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421205174	8.92E-06	8.92E-06	mr1313_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