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Detailed information for vg0514548093:

Variant ID: vg0514548093 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14548093
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

ACGGGTTGAATCAGGATACAATAAAGCATCCTCGATTATAATTTGTGTACCCATTGGGAGTGTAATAGTTGCTCGTCCTGAGCCAACTATCACAGTATCG[C/T]
GCCCAGCGATAGTCAAAACTTTGCCTTCTCTCTTTTTGAGAGTTTGAAAGTATTTGATCTCCCTAAGTATAGAGTTTGTGGTACCACTGTCCACAAGACA

Reverse complement sequence

TGTCTTGTGGACAGTGGTACCACAAACTCTATACTTAGGGAGATCAAATACTTTCAAACTCTCAAAAAGAGAGAAGGCAAAGTTTTGACTATCGCTGGGC[G/A]
CGATACTGTGATAGTTGGCTCAGGACGAGCAACTATTACACTCCCAATGGGTACACAAATTATAATCGAGGATGCTTTATTGTATCCTGATTCAACCCGT

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	79.90%	6.30%	13.01%	0.83%	NA
All Indica	2759	69.80%	9.60%	19.43%	1.12%	NA
All Japonica	1512	99.10%	0.10%	0.20%	0.53%	NA
Aus	269	66.50%	11.20%	22.30%	0.00%	NA
Indica I	595	75.80%	2.00%	18.82%	3.36%	NA
Indica II	465	52.30%	15.70%	30.75%	1.29%	NA
Indica III	913	75.80%	10.50%	13.69%	0.00%	NA
Indica Intermediate	786	68.80%	10.70%	19.85%	0.64%	NA
Temperate Japonica	767	98.60%	0.30%	0.26%	0.91%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	82.20%	1.10%	16.67%	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
vg0514548093	C -> T	LOC_Os05g25100.1	upstream_gene_variant ; 4824.0bp to feature; MODIFIER	silent_mutation	Average:8.927; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N
vg0514548093	C -> T	LOC_Os05g25110.1	intron_variant ; MODIFIER	silent_mutation	Average:8.927; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N
vg0514548093	C -> DEL	N	N	silent_mutation	Average:8.927; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514548093	3.88E-06	NA	mr1962_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