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Detailed information for vg0407237964:

Variant ID: vg0407237964 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7237964
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGAGCCGCCGCCGTGCGCCCAGTTCACCGTGAACCCGACCCGCTGACGCAATAATCCTCTTTTCCTTTTCAAAAATAATTCATTATTGCGTCATAATTC[C/A]
ATTAAAATCCATATAAGTGTTTTAATCCGATTTAATCTTTGAAAATTCATAACTAATTCACTGTAACTCAGTTTAATGTGGTTCAAGTTGCAAAAAATTA

Reverse complement sequence

TAATTTTTTGCAACTTGAACCACATTAAACTGAGTTACAGTGAATTAGTTATGAATTTTCAAAGATTAAATCGGATTAAAACACTTATATGGATTTTAAT[G/T]
GAATTATGACGCAATAATGAATTATTTTTGAAAAGGAAAAGAGGATTATTGCGTCAGCGGGTCGGGTTCACGGTGAACTGGGCGCACGGCGGCGGCTCAC

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	38.50%	1.30%	21.94%	38.19%	NA
All Indica	2759	20.80%	1.20%	33.06%	44.98%	NA
All Japonica	1512	63.70%	1.70%	3.84%	30.75%	NA
Aus	269	71.00%	0.40%	16.36%	12.27%	NA
Indica I	595	10.40%	0.20%	21.85%	67.56%	NA
Indica II	465	17.00%	0.20%	24.09%	58.71%	NA
Indica III	913	28.80%	2.20%	48.52%	20.48%	NA
Indica Intermediate	786	21.60%	1.30%	28.88%	48.22%	NA
Temperate Japonica	767	96.10%	0.00%	0.13%	3.78%	NA
Tropical Japonica	504	11.10%	5.00%	9.92%	74.01%	NA
Japonica Intermediate	241	70.50%	0.40%	2.90%	26.14%	NA
VI/Aromatic	96	56.20%	3.10%	17.71%	22.92%	NA
Intermediate	90	43.30%	1.10%	6.67%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0407237964	C -> DEL	N	N	silent_mutation	Average:15.924; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0407237964	C -> A	LOC_Os04g13110.1	upstream_gene_variant ; 186.0bp to feature; MODIFIER	silent_mutation	Average:15.924; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0407237964	C -> A	LOC_Os04g13120.1	downstream_gene_variant ; 1800.0bp to feature; MODIFIER	silent_mutation	Average:15.924; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0407237964	C -> A	LOC_Os04g13110-LOC_Os04g13120	intergenic_region ; MODIFIER	silent_mutation	Average:15.924; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0407237964	4.16E-06	NA	mr1526	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
vg0407237964	NA	2.93E-07	mr1805	Jap_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
vg0407237964	NA	7.14E-08	mr1807_2	Jap_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