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Detailed information for vg0140721750:

Variant ID: vg0140721750 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 40721750
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

CCTAATTTCGTGCATAATTGCACGTGAAAATCCATTATTAGTTCGTGAGAAAACAACGGCTCCCATCGGATGGCCTATTCAGCCAAAGAAAAAGCCAAAA[T/C]
TTGAATTTTCAAACTTAATTTTGATATTGATTTTGAGATATTTTCAACGTATTTTCTTTTTCAGCATTGGCTTTTAAGTCACCGAGAACACATATATGAA

Reverse complement sequence

TTCATATATGTGTTCTCGGTGACTTAAAAGCCAATGCTGAAAAAGAAAATACGTTGAAAATATCTCAAAATCAATATCAAAATTAAGTTTGAAAATTCAA[A/G]
TTTTGGCTTTTTCTTTGGCTGAATAGGCCATCCGATGGGAGCCGTTGTTTTCTCACGAACTAATAATGGATTTTCACGTGCAATTATGCACGAAATTAGG

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	33.10%	10.80%	2.54%	53.55%	NA
All Indica	2759	1.90%	11.00%	3.52%	83.54%	NA
All Japonica	1512	96.80%	1.50%	0.13%	1.65%	NA
Aus	269	0.70%	29.70%	6.69%	62.83%	NA
Indica I	595	2.70%	10.40%	9.24%	77.65%	NA
Indica II	465	2.20%	1.10%	0.43%	96.34%	NA
Indica III	913	0.50%	13.90%	1.97%	83.57%	NA
Indica Intermediate	786	2.80%	14.00%	2.80%	80.41%	NA
Temperate Japonica	767	98.40%	0.10%	0.26%	1.17%	NA
Tropical Japonica	504	95.40%	2.40%	0.00%	2.18%	NA
Japonica Intermediate	241	94.20%	3.70%	0.00%	2.07%	NA
VI/Aromatic	96	3.10%	94.80%	0.00%	2.08%	NA
Intermediate	90	50.00%	13.30%	3.33%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0140721750	T -> DEL	N	N	silent_mutation	Average:41.667; most accessible tissue: Callus, score: 77.081	N	N	N	N
vg0140721750	T -> C	LOC_Os01g70310.1	upstream_gene_variant ; 4571.0bp to feature; MODIFIER	silent_mutation	Average:41.667; most accessible tissue: Callus, score: 77.081	N	N	N	N
vg0140721750	T -> C	LOC_Os01g70310.2	upstream_gene_variant ; 4571.0bp to feature; MODIFIER	silent_mutation	Average:41.667; most accessible tissue: Callus, score: 77.081	N	N	N	N
vg0140721750	T -> C	LOC_Os01g70320.1	downstream_gene_variant ; 1635.0bp to feature; MODIFIER	silent_mutation	Average:41.667; most accessible tissue: Callus, score: 77.081	N	N	N	N
vg0140721750	T -> C	LOC_Os01g70310-LOC_Os01g70320	intergenic_region ; MODIFIER	silent_mutation	Average:41.667; most accessible tissue: Callus, score: 77.081	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0140721750	NA	5.18E-08	mr1686	Ind_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