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Detailed information for vg0710389112:

Variant ID: vg0710389112 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10389112
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGACACCAAAACCTTCATCTTCCAGAGACTCCTCTTCTGGGTTTGGGAAAAAATTGAGCAAGACTGAGTACAACCACCGTACTCAACAAGACACACCCGC[A/G]
AGTGCATAATAAATGTAAGGGAGTACAAGGGAGTTATAATATAAAGGGTTAGGGTTGCAGTAAACAGCATTTAAAGATACTTAGTTGCTCAAAGCTATTT

Reverse complement sequence

AAATAGCTTTGAGCAACTAAGTATCTTTAAATGCTGTTTACTGCAACCCTAACCCTTTATATTATAACTCCCTTGTACTCCCTTACATTTATTATGCACT[T/C]
GCGGGTGTGTCTTGTTGAGTACGGTGGTTGTACTCAGTCTTGCTCAATTTTTTCCCAAACCCAGAAGAGGAGTCTCTGGAAGATGAAGGTTTTGGTGTCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.90%	0.10%	3.58%	55.37%	NA
All Indica	2759	12.10%	0.20%	4.28%	83.36%	NA
All Japonica	1512	88.80%	0.00%	0.99%	10.25%	NA
Aus	269	63.90%	0.00%	5.95%	30.11%	NA
Indica I	595	15.30%	0.00%	6.22%	78.49%	NA
Indica II	465	10.10%	0.60%	3.44%	85.81%	NA
Indica III	913	5.40%	0.00%	1.97%	92.66%	NA
Indica Intermediate	786	18.80%	0.40%	5.98%	74.81%	NA
Temperate Japonica	767	81.90%	0.00%	0.26%	17.86%	NA
Tropical Japonica	504	94.80%	0.00%	2.38%	2.78%	NA
Japonica Intermediate	241	97.90%	0.00%	0.41%	1.66%	NA
VI/Aromatic	96	41.70%	0.00%	16.67%	41.67%	NA
Intermediate	90	50.00%	0.00%	4.44%	45.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0710389112	A -> DEL	N	N	silent_mutation	Average:11.172; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0710389112	A -> G	LOC_Os07g17600.1	upstream_gene_variant ; 3893.0bp to feature; MODIFIER	silent_mutation	Average:11.172; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0710389112	A -> G	LOC_Os07g17590.1	intron_variant ; MODIFIER	silent_mutation	Average:11.172; 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
vg0710389112	NA	1.11E-10	mr1316	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
vg0710389112	NA	9.36E-11	mr1581	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
vg0710389112	NA	1.43E-07	mr1716	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
vg0710389112	7.56E-07	1.81E-07	mr1672_2	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