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Detailed information for vg0142104276:

Variant ID: vg0142104276 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 42104276
Reference Allele: C	Alternative Allele: A,T
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAAAATCATATTAATCCATTTTCAAGAAAAAAAAAATTAGCTAATACTTAATTAATCATGAGATAAAAGCTACTCCGTTTTACGTGCCAGGGAGGGAAA[C/A,T]
CTCACTCCTGAACGCAACCTTAAAGTAGTTGTGTATTCTCAGCTCCACAAATCAATAGATTTATATCTTTAATCATGTTGATTATATTTGATAAATCATT

Reverse complement sequence

AATGATTTATCAAATATAATCAACATGATTAAAGATATAAATCTATTGATTTGTGGAGCTGAGAATACACAACTACTTTAAGGTTGCGTTCAGGAGTGAG[G/T,A]
TTTCCCTCCCTGGCACGTAAAACGGAGTAGCTTTTATCTCATGATTAATTAAGTATTAGCTAATTTTTTTTTTCTTGAAAATGGATTAATATGATTTTTT

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	94.20%	5.30%	0.15%	0.00%	T: 0.30%
All Indica	2759	99.50%	0.00%	0.04%	0.00%	T: 0.43%
All Japonica	1512	83.20%	16.30%	0.40%	0.00%	T: 0.13%
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.80%	0.00%	0.17%	0.00%	T: 2.02%
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	84.90%	14.20%	0.65%	0.00%	T: 0.26%
Tropical Japonica	504	92.50%	7.50%	0.00%	0.00%	NA
Japonica Intermediate	241	58.50%	41.10%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	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
vg0142104276	C -> T	LOC_Os01g72570-LOC_Os01g72590	intergenic_region ; MODIFIER	silent_mutation	Average:41.894; most accessible tissue: Zhenshan97 root, score: 66.982	N	N	N	N
vg0142104276	C -> A	LOC_Os01g72570-LOC_Os01g72590	intergenic_region ; MODIFIER	silent_mutation	Average:41.894; most accessible tissue: Zhenshan97 root, score: 66.982	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0142104276	2.31E-07	NA	mr1672_2	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