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Detailed information for vg0107383822:

Variant ID: vg0107383822 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 7383822
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATACCCTTATAAACACAATTTTGCTTGGCTTGTTGGGATTGATAAAAAAAAAACCAGTAAACTTATCCTGGTAGGAGCTTCCGCTATATGTTGGGCTCT[A/C]
TGGTTGAATAGAAATGATATGGTTTTTGACAAATCACCATCTATATCTTATATGCAGGTTCTTTTCAGGGCAACACACTAGCTTCGGTCCTGAGCACAAC

Reverse complement sequence

GTTGTGCTCAGGACCGAAGCTAGTGTGTTGCCCTGAAAAGAACCTGCATATAAGATATAGATGGTGATTTGTCAAAAACCATATCATTTCTATTCAACCA[T/G]
AGAGCCCAACATATAGCGGAAGCTCCTACCAGGATAAGTTTACTGGTTTTTTTTTTATCAATCCCAACAAGCCAAGCAAAATTGTGTTTATAAGGGTATT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.70%	0.50%	4.27%	46.49%	NA
All Indica	2759	15.40%	0.90%	7.18%	76.55%	NA
All Japonica	1512	96.90%	0.00%	0.13%	2.98%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	17.00%	0.70%	10.76%	71.60%	NA
Indica II	465	11.20%	0.40%	4.73%	83.66%	NA
Indica III	913	15.70%	1.10%	6.24%	77.00%	NA
Indica Intermediate	786	16.30%	1.10%	7.00%	75.57%	NA
Temperate Japonica	767	97.70%	0.00%	0.00%	2.35%	NA
Tropical Japonica	504	95.20%	0.00%	0.40%	4.37%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	96.90%	0.00%	2.08%	1.04%	NA
Intermediate	90	56.70%	0.00%	0.00%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0107383822	A -> DEL	N	N	silent_mutation	Average:15.577; most accessible tissue: Callus, score: 40.42	N	N	N	N
vg0107383822	A -> C	LOC_Os01g13250.1	upstream_gene_variant ; 2073.0bp to feature; MODIFIER	silent_mutation	Average:15.577; most accessible tissue: Callus, score: 40.42	N	N	N	N
vg0107383822	A -> C	LOC_Os01g13229-LOC_Os01g13250	intergenic_region ; MODIFIER	silent_mutation	Average:15.577; most accessible tissue: Callus, score: 40.42	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0107383822	5.62E-06	NA	mr1109	Ind_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
vg0107383822	4.25E-06	NA	mr1243	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