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Detailed information for vg0618992751:

Variant ID: vg0618992751 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18992751
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGCTGGTCTGACCGCAGGTACTCCGCCGGTCTGACCGCCGCAATGCCACCGGTCTGACCGCCGGTGTTTCACCGGTTAGACCGCCAAACTCGAGAAAAC[G/A]
CAAATCGAAGAACTCTCAAAGTAGATGACCACTTTATTACTTCTCTCTGTGTTACAAAGTGCAACAAGAACACTCCTCACGAATATCTCGACTAAACTCG

Reverse complement sequence

CGAGTTTAGTCGAGATATTCGTGAGGAGTGTTCTTGTTGCACTTTGTAACACAGAGAGAAGTAATAAAGTGGTCATCTACTTTGAGAGTTCTTCGATTTG[C/T]
GTTTTCTCGAGTTTGGCGGTCTAACCGGTGAAACACCGGCGGTCAGACCGGTGGCATTGCGGCGGTCAGACCGGCGGAGTACCTGCGGTCAGACCAGCGA

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	93.30%	3.30%	1.50%	1.95%	NA
All Indica	2759	99.00%	0.50%	0.22%	0.22%	NA
All Japonica	1512	81.70%	8.90%	4.17%	5.22%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.80%	0.00%	0.34%	0.84%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	97.80%	1.70%	0.38%	0.13%	NA
Temperate Japonica	767	88.70%	0.10%	5.22%	6.00%	NA
Tropical Japonica	504	71.40%	25.40%	1.19%	1.98%	NA
Japonica Intermediate	241	80.90%	2.50%	7.05%	9.54%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	90.00%	4.40%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618992751	G -> A	LOC_Os06g32660.1	upstream_gene_variant ; 3025.0bp to feature; MODIFIER	silent_mutation	Average:44.442; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N
vg0618992751	G -> A	LOC_Os06g32650-LOC_Os06g32660	intergenic_region ; MODIFIER	silent_mutation	Average:44.442; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N
vg0618992751	G -> DEL	N	N	silent_mutation	Average:44.442; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618992751	4.64E-06	NA	mr1301	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
vg0618992751	1.31E-06	NA	mr1301_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
vg0618992751	1.32E-06	NA	mr1410_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