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Detailed information for vg0404034503:

Variant ID: vg0404034503 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4034503
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATATGAAAAAAAATATATATCTCAGATATTATTATTTTTATTATGTTGTGATATGTTATCCGTAGCGCACATATATCATGTGTCTCCCCTTCTCTCTA[C/A]
TTTCTATTTTATAGCAAGCAATTCAAGGTAAACATGATGAGTCTGATTTAATTTATAGTTAAGCAAATAATTTTAGATCAATAAAATCCAAACATTTCTA

Reverse complement sequence

TAGAAATGTTTGGATTTTATTGATCTAAAATTATTTGCTTAACTATAAATTAAATCAGACTCATCATGTTTACCTTGAATTGCTTGCTATAAAATAGAAA[G/T]
TAGAGAGAAGGGGAGACACATGATATATGTGCGCTACGGATAACATATCACAACATAATAAAAATAATAATATCTGAGATATATATTTTTTTTCATATAT

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	56.30%	3.30%	1.69%	38.66%	NA
All Indica	2759	48.10%	5.50%	1.85%	44.58%	NA
All Japonica	1512	67.60%	0.20%	1.72%	30.49%	NA
Aus	269	63.20%	0.00%	0.37%	36.43%	NA
Indica I	595	57.60%	6.10%	2.35%	33.95%	NA
Indica II	465	70.80%	0.40%	0.86%	27.96%	NA
Indica III	913	26.90%	9.70%	1.86%	61.45%	NA
Indica Intermediate	786	51.90%	3.20%	2.04%	42.88%	NA
Temperate Japonica	767	76.00%	0.30%	1.96%	21.77%	NA
Tropical Japonica	504	58.30%	0.20%	1.19%	40.28%	NA
Japonica Intermediate	241	60.20%	0.00%	2.07%	37.76%	NA
VI/Aromatic	96	91.70%	1.00%	0.00%	7.29%	NA
Intermediate	90	62.20%	1.10%	2.22%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404034503	C -> DEL	N	N	silent_mutation	Average:31.456; most accessible tissue: Callus, score: 60.394	N	N	N	N
vg0404034503	C -> A	LOC_Os04g07580.1	upstream_gene_variant ; 501.0bp to feature; MODIFIER	silent_mutation	Average:31.456; most accessible tissue: Callus, score: 60.394	N	N	N	N
vg0404034503	C -> A	LOC_Os04g07590.1	downstream_gene_variant ; 2948.0bp to feature; MODIFIER	silent_mutation	Average:31.456; most accessible tissue: Callus, score: 60.394	N	N	N	N
vg0404034503	C -> A	LOC_Os04g07580-LOC_Os04g07590	intergenic_region ; MODIFIER	silent_mutation	Average:31.456; most accessible tissue: Callus, score: 60.394	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404034503	2.65E-06	2.65E-06	mr1175	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