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Detailed information for vg0141267197:

Variant ID: vg0141267197 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 41267197
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, T: 0.32, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

GCCCACGTGAAATAATGCATGTAGCCTTGTTATATGCTATTTATGAAATATAGATTTTGCCTTTCTATCAGCCTGGTATTCTGAACTATAATCTGAAATT[T/C]
AATCTATCGAATAGCAACATAGCATGAGTGTGTCATGACTCATGAGGCTAGTGTTTGACTGAATTTGTGCTACATTTATATGGTGGATTCACTTCGCGAT

Reverse complement sequence

ATCGCGAAGTGAATCCACCATATAAATGTAGCACAAATTCAGTCAAACACTAGCCTCATGAGTCATGACACACTCATGCTATGTTGCTATTCGATAGATT[A/G]
AATTTCAGATTATAGTTCAGAATACCAGGCTGATAGAAAGGCAAAATCTATATTTCATAAATAGCATATAACAAGGCTACATGCATTATTTCACGTGGGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.90%	49.70%	0.08%	0.32%	NA
All Indica	2759	68.60%	30.90%	0.00%	0.47%	NA
All Japonica	1512	5.40%	94.40%	0.20%	0.00%	NA
Aus	269	97.00%	3.00%	0.00%	0.00%	NA
Indica I	595	39.80%	59.30%	0.00%	0.84%	NA
Indica II	465	87.50%	11.80%	0.00%	0.65%	NA
Indica III	913	80.70%	19.30%	0.00%	0.00%	NA
Indica Intermediate	786	65.30%	34.10%	0.00%	0.64%	NA
Temperate Japonica	767	1.20%	98.80%	0.00%	0.00%	NA
Tropical Japonica	504	6.90%	92.50%	0.60%	0.00%	NA
Japonica Intermediate	241	15.80%	84.20%	0.00%	0.00%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	43.30%	53.30%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0141267197	T -> DEL	N	N	silent_mutation	Average:53.73; most accessible tissue: Callus, score: 88.122	N	N	N	N
vg0141267197	T -> C	LOC_Os01g71300.1	intron_variant ; MODIFIER	silent_mutation	Average:53.73; most accessible tissue: Callus, score: 88.122	N	N	N	N
vg0141267197	T -> C	LOC_Os01g71300.3	intron_variant ; MODIFIER	silent_mutation	Average:53.73; most accessible tissue: Callus, score: 88.122	N	N	N	N
vg0141267197	T -> C	LOC_Os01g71300.2	intron_variant ; MODIFIER	silent_mutation	Average:53.73; most accessible tissue: Callus, score: 88.122	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0141267197	6.55E-08	8.96E-07	mr1425_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
vg0141267197	2.01E-07	7.08E-08	mr1750_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
vg0141267197	NA	1.68E-06	mr1974_2	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