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Detailed information for vg0618469761:

Variant ID: vg0618469761 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18469761
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTCGTTTAAAGGTGTTAGTTTTTTTTTTTTCATTTTATGAAGGTGGGAAAAGCACTATAGGTACCGGTTTAATCACTTCCGTTACCTATAGTGGCAACA[C/A]
CTATTTGATATTTTGTATGAGTGACTATGAGTATTGTTAAGTCAGATTTGACATCACATATGCTTTAATTTTTTTTAATAAAACCACTCGGCTGGTTGAT

Reverse complement sequence

ATCAACCAGCCGAGTGGTTTTATTAAAAAAAATTAAAGCATATGTGATGTCAAATCTGACTTAACAATACTCATAGTCACTCATACAAAATATCAAATAG[G/T]
TGTTGCCACTATAGGTAACGGAAGTGATTAAACCGGTACCTATAGTGCTTTTCCCACCTTCATAAAATGAAAAAAAAAAAACTAACACCTTTAAACGAAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.60%	0.20%	1.90%	30.22%	NA
All Indica	2759	54.00%	0.40%	3.01%	42.62%	NA
All Japonica	1512	93.50%	0.00%	0.33%	6.22%	NA
Aus	269	47.60%	0.00%	0.00%	52.42%	NA
Indica I	595	64.90%	0.00%	2.86%	32.27%	NA
Indica II	465	50.10%	0.00%	2.37%	47.53%	NA
Indica III	913	45.70%	0.90%	3.61%	49.84%	NA
Indica Intermediate	786	57.60%	0.40%	2.80%	39.19%	NA
Temperate Japonica	767	95.00%	0.00%	0.26%	4.69%	NA
Tropical Japonica	504	91.50%	0.00%	0.60%	7.94%	NA
Japonica Intermediate	241	92.50%	0.00%	0.00%	7.47%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	NA
Intermediate	90	82.20%	0.00%	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
vg0618469761	C -> A	LOC_Os06g31800.1	upstream_gene_variant ; 1644.0bp to feature; MODIFIER	silent_mutation	Average:7.948; most accessible tissue: Callus, score: 35.491	N	N	N	N
vg0618469761	C -> A	LOC_Os06g31810.1	downstream_gene_variant ; 3935.0bp to feature; MODIFIER	silent_mutation	Average:7.948; most accessible tissue: Callus, score: 35.491	N	N	N	N
vg0618469761	C -> A	LOC_Os06g31800-LOC_Os06g31810	intergenic_region ; MODIFIER	silent_mutation	Average:7.948; most accessible tissue: Callus, score: 35.491	N	N	N	N
vg0618469761	C -> DEL	N	N	silent_mutation	Average:7.948; most accessible tissue: Callus, score: 35.491	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618469761	4.68E-06	4.68E-06	mr1945	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