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Detailed information for vg0630599588:

Variant ID: vg0630599588 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 30599588
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATATATATATATATATATATATATATATATGTAAAATTGATCTGGAATGTGGCAGTTACATGGGCCTGAATGATGTGAGGAGAAAATTTGTTCTACTTG[C/G]
TAGGACATGATGTGATCTGGACAGGAAAACGGAAAACGTGGAGCAATTTGGGAGGGGGCGATATGGAGGAATCGGACCGGAAAATCGTAAAAAAATACGC

Reverse complement sequence

GCGTATTTTTTTACGATTTTCCGGTCCGATTCCTCCATATCGCCCCCTCCCAAATTGCTCCACGTTTTCCGTTTTCCTGTCCAGATCACATCATGTCCTA[G/C]
CAAGTAGAACAAATTTTCTCCTCACATCATTCAGGCCCATGTAACTGCCACATTCCAGATCAATTTTACATATATATATATATATATATATATATATATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.90%	1.90%	1.18%	15.02%	NA
All Indica	2759	86.20%	0.10%	0.36%	13.34%	NA
All Japonica	1512	75.70%	5.60%	3.04%	15.67%	NA
Aus	269	74.30%	0.00%	0.00%	25.65%	NA
Indica I	595	99.70%	0.00%	0.00%	0.34%	NA
Indica II	465	83.70%	0.00%	0.22%	16.13%	NA
Indica III	913	77.70%	0.20%	0.77%	21.36%	NA
Indica Intermediate	786	87.40%	0.10%	0.25%	12.21%	NA
Temperate Japonica	767	96.00%	1.30%	1.30%	1.43%	NA
Tropical Japonica	504	47.60%	13.30%	5.36%	33.73%	NA
Japonica Intermediate	241	69.70%	3.30%	3.73%	23.24%	NA
VI/Aromatic	96	71.90%	0.00%	0.00%	28.12%	NA
Intermediate	90	88.90%	1.10%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0630599588	C -> G	LOC_Os06g50539.1	upstream_gene_variant ; 632.0bp to feature; MODIFIER	silent_mutation	Average:55.351; most accessible tissue: Zhenshan97 flower, score: 81.047	N	N	N	N
vg0630599588	C -> G	LOC_Os06g50539.3	upstream_gene_variant ; 632.0bp to feature; MODIFIER	silent_mutation	Average:55.351; most accessible tissue: Zhenshan97 flower, score: 81.047	N	N	N	N
vg0630599588	C -> G	LOC_Os06g50530.1	downstream_gene_variant ; 1530.0bp to feature; MODIFIER	silent_mutation	Average:55.351; most accessible tissue: Zhenshan97 flower, score: 81.047	N	N	N	N
vg0630599588	C -> G	LOC_Os06g50530-LOC_Os06g50539	intergenic_region ; MODIFIER	silent_mutation	Average:55.351; most accessible tissue: Zhenshan97 flower, score: 81.047	N	N	N	N
vg0630599588	C -> DEL	N	N	silent_mutation	Average:55.351; most accessible tissue: Zhenshan97 flower, score: 81.047	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0630599588	3.74E-07	1.23E-07	mr1113	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
vg0630599588	NA	2.73E-07	mr1414	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
vg0630599588	8.35E-06	5.60E-07	mr1682	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
vg0630599588	NA	3.31E-06	mr1850_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