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Detailed information for vg0514013284:

Variant ID: vg0514013284 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14013284
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCTGTACGTGTGGATACCGGTAGAGGCGCCGCTGGTTTGCGGTGCTGATCGGCGTGGGGGTACGGCGAGGAGAACACATGAGGAGGAGAAGGTCGAGCC[G/A]
GTGCGATCGACTACTTCCTCTACATCGACGCGCGCTACTTTGCGAGAGTTCCTTCGACTTCTCACCGTCTTCTTCCGCTTTGCAGCGCGTCGAGTGGTAA

Reverse complement sequence

TTACCACTCGACGCGCTGCAAAGCGGAAGAAGACGGTGAGAAGTCGAAGGAACTCTCGCAAAGTAGCGCGCGTCGATGTAGAGGAAGTAGTCGATCGCAC[C/T]
GGCTCGACCTTCTCCTCCTCATGTGTTCTCCTCGCCGTACCCCCACGCCGATCAGCACCGCAAACCAGCGGCGCCTCTACCGGTATCCACACGTACAGGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.20%	11.70%	0.17%	0.00%	NA
All Indica	2759	88.00%	11.80%	0.25%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.07%	0.00%	NA
Aus	269	23.00%	77.00%	0.00%	0.00%	NA
Indica I	595	81.20%	17.80%	1.01%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	84.00%	16.00%	0.00%	0.00%	NA
Indica Intermediate	786	91.20%	8.70%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.20%	1.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0514013284	G -> A	LOC_Os05g24220.1	downstream_gene_variant ; 1561.0bp to feature; MODIFIER	silent_mutation	Average:60.818; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N
vg0514013284	G -> A	LOC_Os05g24230.1	intron_variant ; MODIFIER	silent_mutation	Average:60.818; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514013284	NA	8.78E-06	mr1344_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
vg0514013284	1.12E-06	NA	mr1713_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