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Detailed information for vg0910217057:

Variant ID: vg0910217057 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10217057
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATGAGCTAGGAGACAGATTGGCCAATTTCGGTTCAAAACGGGAAGCAGCCCTAATCCAGTCGGCTCAGTATTTACAAGGGTTGCACCGTTATCATAATC[G/A]
GAATGTTCGATCGCGAGCCTTTCTAGTCGGCGACCTGGTTTTGAGGAGAATTCAAACTACACAGGATCGGCATAAGTTATCTCCCTTGTGGGAAGGACCG

Reverse complement sequence

CGGTCCTTCCCACAAGGGAGATAACTTATGCCGATCCTGTGTAGTTTGAATTCTCCTCAAAACCAGGTCGCCGACTAGAAAGGCTCGCGATCGAACATTC[C/T]
GATTATGATAACGGTGCAACCCTTGTAAATACTGAGCCGACTGGATTAGGGCTGCTTCCCGTTTTGAACCGAAATTGGCCAATCTGTCTCCTAGCTCATT

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	69.50%	17.60%	11.19%	1.71%	NA
All Indica	2759	78.80%	0.70%	17.80%	2.65%	NA
All Japonica	1512	50.60%	48.10%	1.12%	0.20%	NA
Aus	269	90.00%	6.30%	3.72%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	58.10%	1.30%	29.89%	10.75%	NA
Indica III	913	74.40%	0.70%	24.86%	0.11%	NA
Indica Intermediate	786	80.40%	1.00%	15.78%	2.80%	NA
Temperate Japonica	767	71.60%	28.20%	0.13%	0.13%	NA
Tropical Japonica	504	19.80%	76.80%	3.17%	0.20%	NA
Japonica Intermediate	241	48.10%	51.50%	0.00%	0.41%	NA
VI/Aromatic	96	54.20%	39.60%	5.21%	1.04%	NA
Intermediate	90	56.70%	32.20%	6.67%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910217057	G -> DEL	LOC_Os09g16680.1	N	frameshift_variant	Average:28.269; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg0910217057	G -> A	LOC_Os09g16680.1	missense_variant ; p.Arg495Gln; MODERATE	stop_gained	Average:28.269; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg0910217057	G -> A	LOC_Os09g16680.1	missense_variant ; p.Arg495Gln; MODERATE	nonsynonymous_codon ; R495Q	Average:28.269; most accessible tissue: Zhenshan97 root, score: 39.742	unknown	unknown	TOLERATED	0.06

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910217057	NA	4.47E-13	mr1070	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
vg0910217057	3.62E-06	1.25E-13	mr1128	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
vg0910217057	NA	2.29E-12	mr1454	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