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Detailed information for vg0504438915:

Variant ID: vg0504438915 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 4438915
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCTTTGACTTGACAACCACGTCATCAATATAAACTTCAACCAACCAGCCGATCAGATCATGGAATATGTAATTCATGGCTCGCTGATACGTAGCTCCA[G/A]
CACTCTTCAAGCCGAAAGTCATCACAACCCACTCAAACAAGCCGATTGCAACAGGACACCTGAAAGCTGTCTTATGAATATCTTCTTCTGCCATAAAGAT

Reverse complement sequence

ATCTTTATGGCAGAAGAAGATATTCATAAGACAGCTTTCAGGTGTCCTGTTGCAATCGGCTTGTTTGAGTGGGTTGTGATGACTTTCGGCTTGAAGAGTG[C/T]
TGGAGCTACGTATCAGCGAGCCATGAATTACATATTCCATGATCTGATCGGCTGGTTGGTTGAAGTTTATATTGATGACGTGGTTGTCAAGTCAAAGGAA

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	60.50%	0.20%	5.06%	34.32%	NA
All Indica	2759	35.20%	0.30%	8.48%	56.07%	NA
All Japonica	1512	99.10%	0.00%	0.00%	0.86%	NA
Aus	269	84.00%	0.00%	1.12%	14.87%	NA
Indica I	595	46.40%	0.50%	3.36%	49.75%	NA
Indica II	465	31.80%	0.60%	6.88%	60.65%	NA
Indica III	913	26.60%	0.00%	14.46%	58.93%	NA
Indica Intermediate	786	38.50%	0.30%	6.36%	54.83%	NA
Temperate Japonica	767	98.70%	0.00%	0.00%	1.30%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	91.70%	0.00%	0.00%	8.33%	NA
Intermediate	90	82.20%	0.00%	2.22%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0504438915	G -> DEL	LOC_Os05g08150.1	N	frameshift_variant	Average:9.424; most accessible tissue: Zhenshan97 young leaf, score: 18.918	N	N	N	N
vg0504438915	G -> A	LOC_Os05g08150.1	missense_variant ; p.Ala1021Val; MODERATE	nonsynonymous_codon ; A1021V	Average:9.424; most accessible tissue: Zhenshan97 young leaf, score: 18.918	benign	0.572	TOLERATED	0.07

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0504438915	1.41E-06	1.40E-06	mr1464	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
vg0504438915	5.70E-06	5.70E-06	mr1464	Ind_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