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Detailed information for vg0614119998:

Variant ID: vg0614119998 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14119998
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGGTCTATGCGGCTTTCGGATTCACCTAGGCACGAGAGGGGACTGCCCGTTGCCTTGCGAGGAGTGGGGGTGAAACCTGCGGTGTGGTGTGTTTAGTTA[G/T]
AGGGGGTTATGCGAAGGGTCCTGTCACGGTCTCTTTCCGGTATTTGTGGTGTTATGTCAGCGCACGGTAACGTATCGTGGGGCTGTGTCTTGTGGGTACA

Reverse complement sequence

TGTACCCACAAGACACAGCCCCACGATACGTTACCGTGCGCTGACATAACACCACAAATACCGGAAAGAGACCGTGACAGGACCCTTCGCATAACCCCCT[C/A]
TAACTAAACACACCACACCGCAGGTTTCACCCCCACTCCTCGCAAGGCAACGGGCAGTCCCCTCTCGTGCCTAGGTGAATCCGAAAGCCGCATAGACCAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.20%	1.70%	1.02%	1.06%	NA
All Indica	2759	99.70%	0.20%	0.11%	0.04%	NA
All Japonica	1512	94.10%	4.60%	1.19%	0.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	99.80%	0.10%	0.11%	0.00%	NA
Indica Intermediate	786	99.40%	0.50%	0.00%	0.13%	NA
Temperate Japonica	767	99.50%	0.10%	0.39%	0.00%	NA
Tropical Japonica	504	84.70%	12.90%	2.38%	0.00%	NA
Japonica Intermediate	241	96.70%	1.70%	1.24%	0.41%	NA
VI/Aromatic	96	27.10%	0.00%	27.08%	45.83%	NA
Intermediate	90	88.90%	5.60%	1.11%	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
vg0614119998	G -> T	LOC_Os06g24130.1	upstream_gene_variant ; 1297.0bp to feature; MODIFIER	silent_mutation	Average:58.425; most accessible tissue: Zhenshan97 flag leaf, score: 75.761	N	N	N	N
vg0614119998	G -> T	LOC_Os06g24130-LOC_Os06g24150	intergenic_region ; MODIFIER	silent_mutation	Average:58.425; most accessible tissue: Zhenshan97 flag leaf, score: 75.761	N	N	N	N
vg0614119998	G -> DEL	N	N	silent_mutation	Average:58.425; most accessible tissue: Zhenshan97 flag leaf, score: 75.761	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614119998	NA	3.94E-07	mr1217_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
vg0614119998	8.43E-07	3.01E-09	mr1218_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
vg0614119998	6.20E-06	1.54E-09	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