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Detailed information for vg0310496278:

Variant ID: vg0310496278 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 10496278
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTCTTCATGTAGATATGAATTAGTGTTATATATTTGTCAAGCAAATTTGACACCAAGTGAAATTATTTTAAAAATGATCATGACATTAATTATTATAT[G/A]
TTAGCTAAATTATTTGAAAAATAATTATGACATTACATATTATATGTCGGCACCATATGTCGTGATGAATTTAGCAGTTCCATATAACTATTATAAGTGA

Reverse complement sequence

TCACTTATAATAGTTATATGGAACTGCTAAATTCATCACGACATATGGTGCCGACATATAATATGTAATGTCATAATTATTTTTCAAATAATTTAGCTAA[C/T]
ATATAATAATTAATGTCATGATCATTTTTAAAATAATTTCACTTGGTGTCAAATTTGCTTGACAAATATATAACACTAATTCATATCTACATGAAGAAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.20%	5.50%	1.06%	1.23%	NA
All Indica	2759	99.70%	0.20%	0.07%	0.04%	NA
All Japonica	1512	77.40%	16.20%	2.91%	3.44%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.30%	0.25%	0.13%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	43.10%	39.90%	7.74%	9.33%	NA
Japonica Intermediate	241	79.70%	16.20%	2.07%	2.07%	NA
VI/Aromatic	96	94.80%	4.20%	0.00%	1.04%	NA
Intermediate	90	84.40%	6.70%	4.44%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0310496278	G -> A	LOC_Os03g18729-LOC_Os03g18740	intergenic_region ; MODIFIER	silent_mutation	Average:30.125; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N
vg0310496278	G -> DEL	N	N	silent_mutation	Average:30.125; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0310496278	NA	2.14E-07	mr1696	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
vg0310496278	NA	1.43E-09	mr1852	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
vg0310496278	NA	9.50E-06	mr1397_2	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
vg0310496278	NA	1.64E-07	mr1696_2	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
vg0310496278	NA	3.83E-13	mr1864_2	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
vg0310496278	NA	2.40E-06	mr1923_2	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