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Detailed information for vg0135107915:

Variant ID: vg0135107915 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 35107915
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACGATTTAAAAACTTTTAAGTTCAGATTTAAAATTTTTTATTTTTTTTCAAATCTTGATTTGAAAGTTTTCGAATCTCGATTTGAAAGTTTTCGAATCT[T/C]
GATTTGAAAGTTTTCGAATCTCAAATTGAAAGTTTTCAAATTTTTCAAATCTGGACTTGAAAGTTTTCGAATCTCGATTCTCGAGTTGAAAGTTTCGATT

Reverse complement sequence

AATCGAAACTTTCAACTCGAGAATCGAGATTCGAAAACTTTCAAGTCCAGATTTGAAAAATTTGAAAACTTTCAATTTGAGATTCGAAAACTTTCAAATC[A/G]
AGATTCGAAAACTTTCAAATCGAGATTCGAAAACTTTCAAATCAAGATTTGAAAAAAAATAAAAAATTTTAAATCTGAACTTAAAAGTTTTTAAATCGTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.60%	0.10%	0.30%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.00%	NA
All Japonica	1512	98.90%	0.20%	0.86%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	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	98.60%	0.30%	1.17%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0135107915	T -> C	LOC_Os01g60710.1	downstream_gene_variant ; 4004.0bp to feature; MODIFIER	N	Average:25.642; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N
vg0135107915	T -> C	LOC_Os01g60700-LOC_Os01g60710	intergenic_region ; MODIFIER	N	Average:25.642; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0135107915	2.75E-06	NA	mr1842_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