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Detailed information for vg0403769688:

Variant ID: vg0403769688 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3769688
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGCATCTGGTATATATACATCGGTTACAGTGGAAGTCAAATCAGCTCCGCTGATTTTTTTTTTCCGTATATTTATCCTCATTTTTGCATGTCACTTAGA[T/C]
AGGTATCAAAAATTTGAAAAAAAAATTCATATGATATATCAATATAAAATATATTATCAAATATGAAAATTCAAATTCAACCTATGCAAGTAAAAAAATA

Reverse complement sequence

TATTTTTTTACTTGCATAGGTTGAATTTGAATTTTCATATTTGATAATATATTTTATATTGATATATCATATGAATTTTTTTTTCAAATTTTTGATACCT[A/G]
TCTAAGTGACATGCAAAAATGAGGATAAATATACGGAAAAAAAAAATCAGCGGAGCTGATTTGACTTCCACTGTAACCGATGTATATATACCAGATGCGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.50%	5.40%	7.72%	6.37%	NA
All Indica	2759	94.60%	1.90%	1.56%	1.92%	NA
All Japonica	1512	51.40%	12.90%	19.51%	16.20%	NA
Aus	269	92.60%	2.20%	4.46%	0.74%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	89.50%	5.20%	3.01%	2.37%	NA
Indica III	913	95.10%	0.80%	0.99%	3.18%	NA
Indica Intermediate	786	93.50%	2.40%	2.42%	1.65%	NA
Temperate Japonica	767	67.40%	12.50%	16.56%	3.52%	NA
Tropical Japonica	504	26.00%	14.10%	24.80%	35.12%	NA
Japonica Intermediate	241	53.50%	11.60%	17.84%	17.01%	NA
VI/Aromatic	96	90.60%	1.00%	8.33%	0.00%	NA
Intermediate	90	88.90%	2.20%	7.78%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403769688	T -> C	LOC_Os04g07110.1	downstream_gene_variant ; 1224.0bp to feature; MODIFIER	silent_mutation	Average:22.041; most accessible tissue: Callus, score: 55.505	N	N	N	N
vg0403769688	T -> C	LOC_Os04g07110-LOC_Os04g07120	intergenic_region ; MODIFIER	silent_mutation	Average:22.041; most accessible tissue: Callus, score: 55.505	N	N	N	N
vg0403769688	T -> DEL	N	N	silent_mutation	Average:22.041; most accessible tissue: Callus, score: 55.505	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403769688	1.72E-06	1.12E-07	mr1679_2	Jap_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