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Detailed information for vg0523655696:

Variant ID: vg0523655696 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 23655696
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAAATTGGACAGGGGTCTTCTGCCATGATTTGGGTGATACATATCTTCATGTAACAGAACTGTATGACCAATACTTCTACATAATTTATTTGCCATAT[C/T]
CTCACTTTCAGTTTGGTTGTCATAATAGGAACTATGAATGCTAGTGGTCATAGAAAACGGTTCTATAGTTAAATGCTGATGACTATGTTTTCCATAGCTG

Reverse complement sequence

CAGCTATGGAAAACATAGTCATCAGCATTTAACTATAGAACCGTTTTCTATGACCACTAGCATTCATAGTTCCTATTATGACAACCAAACTGAAAGTGAG[G/A]
ATATGGCAAATAAATTATGTAGAAGTATTGGTCATACAGTTCTGTTACATGAAGATATGTATCACCCAAATCATGGCAGAAGACCCCTGTCCAATTTTTT

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	95.50%	4.50%	0.02%	0.00%	NA
All Indica	2759	99.40%	0.60%	0.04%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	38.70%	61.30%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	1.10%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	67.70%	32.30%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0523655696	C -> T	LOC_Os05g40270.1	intron_variant ; MODIFIER	silent_mutation	Average:45.467; most accessible tissue: Callus, score: 80.693	N	N	N	N
vg0523655696	C -> T	LOC_Os05g40270.10	intron_variant ; MODIFIER	silent_mutation	Average:45.467; most accessible tissue: Callus, score: 80.693	N	N	N	N
vg0523655696	C -> T	LOC_Os05g40270.5	intron_variant ; MODIFIER	silent_mutation	Average:45.467; most accessible tissue: Callus, score: 80.693	N	N	N	N
vg0523655696	C -> T	LOC_Os05g40270.6	intron_variant ; MODIFIER	silent_mutation	Average:45.467; most accessible tissue: Callus, score: 80.693	N	N	N	N
vg0523655696	C -> T	LOC_Os05g40270.8	intron_variant ; MODIFIER	silent_mutation	Average:45.467; most accessible tissue: Callus, score: 80.693	N	N	N	N
vg0523655696	C -> T	LOC_Os05g40270.9	intron_variant ; MODIFIER	silent_mutation	Average:45.467; most accessible tissue: Callus, score: 80.693	N	N	N	N
vg0523655696	C -> T	LOC_Os05g40270.2	intron_variant ; MODIFIER	silent_mutation	Average:45.467; most accessible tissue: Callus, score: 80.693	N	N	N	N
vg0523655696	C -> T	LOC_Os05g40270.3	intron_variant ; MODIFIER	silent_mutation	Average:45.467; most accessible tissue: Callus, score: 80.693	N	N	N	N
vg0523655696	C -> T	LOC_Os05g40270.7	intron_variant ; MODIFIER	silent_mutation	Average:45.467; most accessible tissue: Callus, score: 80.693	N	N	N	N
vg0523655696	C -> T	LOC_Os05g40270.4	intron_variant ; MODIFIER	silent_mutation	Average:45.467; most accessible tissue: Callus, score: 80.693	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0523655696	2.86E-06	NA	mr1587_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
vg0523655696	NA	2.50E-09	mr1612_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