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Detailed information for vg0717183599:

Variant ID: vg0717183599 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 17183599
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAAAAAAAGGAAGGAGAGGAGGGAGAGGAGGGGAGTTAGAGATAAGGAAAGAGATAAGAAGTTAGAGAGGAAAACCGGGACTAAAAACCTATTTTTAGT[T/C]
CCGGTTGGTGTTATTAACCGGGACTAAAGATCCTAGGGCCCTGACACGGCCTGACATGGAATCAACCGGGACTAAAAATGATCTTTAGTCCCGGTTGGTA

Reverse complement sequence

TACCAACCGGGACTAAAGATCATTTTTAGTCCCGGTTGATTCCATGTCAGGCCGTGTCAGGGCCCTAGGATCTTTAGTCCCGGTTAATAACACCAACCGG[A/G]
ACTAAAAATAGGTTTTTAGTCCCGGTTTTCCTCTCTAACTTCTTATCTCTTTCCTTATCTCTAACTCCCCTCCTCTCCCTCCTCTCCTTCCTTTTTTTCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.10%	3.60%	3.36%	1.99%	NA
All Indica	2759	96.10%	0.10%	0.36%	3.41%	NA
All Japonica	1512	80.50%	10.60%	8.93%	0.00%	NA
Aus	269	97.40%	0.00%	2.60%	0.00%	NA
Indica I	595	98.70%	0.00%	0.17%	1.18%	NA
Indica II	465	90.80%	0.40%	0.43%	8.39%	NA
Indica III	913	97.40%	0.10%	0.22%	2.30%	NA
Indica Intermediate	786	95.90%	0.00%	0.64%	3.44%	NA
Temperate Japonica	767	67.40%	20.10%	12.52%	0.00%	NA
Tropical Japonica	504	95.60%	0.40%	3.97%	0.00%	NA
Japonica Intermediate	241	90.50%	1.70%	7.88%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	87.80%	5.60%	6.67%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0717183599	T -> DEL	N	N	silent_mutation	Average:47.702; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0717183599	T -> C	LOC_Os07g29310.1	upstream_gene_variant ; 3074.0bp to feature; MODIFIER	silent_mutation	Average:47.702; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0717183599	T -> C	LOC_Os07g29300-LOC_Os07g29310	intergenic_region ; MODIFIER	silent_mutation	Average:47.702; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0717183599	NA	4.73E-07	mr1354	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
vg0717183599	NA	2.92E-06	mr1011_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
vg0717183599	1.80E-07	1.80E-07	mr1568_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