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Detailed information for vg0410246763:

Variant ID: vg0410246763 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 10246763
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATCTACTCCTTCCTAATCTCTGATTTTTGTTTCCTTCTCTCTCAGCGAAACTCACGCCCTCATAGCCCTAACGCCAAAACTACTCCATCTTCTTCCTC[A/C]
AGCCCTTCGTCCTCACGAACCACAACCCTAGACACCTCCATTGCTGGCGAATTGATCATGGCGGACCTTCCCGAGGAACTTTACTACCCACAATACTTTC

Reverse complement sequence

GAAAGTATTGTGGGTAGTAAAGTTCCTCGGGAAGGTCCGCCATGATCAATTCGCCAGCAATGGAGGTGTCTAGGGTTGTGGTTCGTGAGGACGAAGGGCT[T/G]
GAGGAAGAAGATGGAGTAGTTTTGGCGTTAGGGCTATGAGGGCGTGAGTTTCGCTGAGAGAGAAGGAAACAAAAATCAGAGATTAGGAAGGAGTAGATAT

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	37.80%	9.40%	15.81%	36.97%	NA
All Indica	2759	5.50%	14.80%	24.18%	55.49%	NA
All Japonica	1512	98.90%	0.20%	0.26%	0.66%	NA
Aus	269	1.90%	10.80%	24.91%	62.45%	NA
Indica I	595	6.60%	19.80%	43.03%	30.59%	NA
Indica II	465	7.70%	6.90%	22.15%	63.23%	NA
Indica III	913	2.20%	14.10%	17.31%	66.37%	NA
Indica Intermediate	786	7.40%	16.40%	19.08%	57.12%	NA
Temperate Japonica	767	99.60%	0.10%	0.00%	0.26%	NA
Tropical Japonica	504	98.60%	0.40%	0.40%	0.60%	NA
Japonica Intermediate	241	97.10%	0.00%	0.83%	2.07%	NA
VI/Aromatic	96	86.50%	0.00%	3.12%	10.42%	NA
Intermediate	90	57.80%	4.40%	6.67%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0410246763	A -> C	LOC_Os04g18540.1	upstream_gene_variant ; 2508.0bp to feature; MODIFIER	silent_mutation	Average:16.854; most accessible tissue: Callus, score: 62.794	N	N	N	N
vg0410246763	A -> C	LOC_Os04g18550.1	upstream_gene_variant ; 304.0bp to feature; MODIFIER	silent_mutation	Average:16.854; most accessible tissue: Callus, score: 62.794	N	N	N	N
vg0410246763	A -> C	LOC_Os04g18559.1	downstream_gene_variant ; 2873.0bp to feature; MODIFIER	silent_mutation	Average:16.854; most accessible tissue: Callus, score: 62.794	N	N	N	N
vg0410246763	A -> C	LOC_Os04g18540-LOC_Os04g18550	intergenic_region ; MODIFIER	silent_mutation	Average:16.854; most accessible tissue: Callus, score: 62.794	N	N	N	N
vg0410246763	A -> DEL	N	N	silent_mutation	Average:16.854; most accessible tissue: Callus, score: 62.794	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0410246763	8.80E-08	8.80E-08	mr1335_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