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Detailed information for vg0130684898:

Variant ID: vg0130684898 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 30684898
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCCCGACGTGGGAGGAGCATGGACCGTCCGATCTGATGAACGGTCTCGATTGATCCTAACCTAGATAAATACCCGTAACCCTAACCCTAACCCTAAAAT[C/A]
TCTCTCTCTCTCTCTCGATCCCCTAACACGATCTCTCTCTCTCTCTCTTTCTTTCTCGTAAAGCAATGGCGCCGGCGGCGACTATTCCAACAGGCGATGA

Reverse complement sequence

TCATCGCCTGTTGGAATAGTCGCCGCCGGCGCCATTGCTTTACGAGAAAGAAAGAGAGAGAGAGAGAGATCGTGTTAGGGGATCGAGAGAGAGAGAGAGA[G/T]
ATTTTAGGGTTAGGGTTAGGGTTACGGGTATTTATCTAGGTTAGGATCAATCGAGACCGTTCATCAGATCGGACGGTCCATGCTCCTCCCACGTCGGGCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.30%	0.90%	1.12%	1.69%	NA
All Indica	2759	96.80%	1.40%	1.59%	0.18%	NA
All Japonica	1512	94.40%	0.10%	0.53%	4.96%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	98.50%	0.80%	0.67%	0.00%	NA
Indica II	465	94.40%	2.60%	2.37%	0.65%	NA
Indica III	913	96.10%	1.60%	2.30%	0.00%	NA
Indica Intermediate	786	97.70%	1.00%	1.02%	0.25%	NA
Temperate Japonica	767	95.40%	0.00%	0.78%	3.78%	NA
Tropical Japonica	504	99.20%	0.00%	0.20%	0.60%	NA
Japonica Intermediate	241	81.30%	0.40%	0.41%	17.84%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	1.11%	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
vg0130684898	C -> A	LOC_Os01g53420.1	downstream_gene_variant ; 4949.0bp to feature; MODIFIER	silent_mutation	Average:67.386; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg0130684898	C -> A	LOC_Os01g53390-LOC_Os01g53420	intergenic_region ; MODIFIER	silent_mutation	Average:67.386; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg0130684898	C -> DEL	N	N	silent_mutation	Average:67.386; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0130684898	2.87E-06	8.06E-08	mr1197	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
vg0130684898	4.62E-06	4.61E-06	mr1197	Ind_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