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Detailed information for vg0217179848:

Variant ID: vg0217179848 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17179848
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACCGGGCTGCGCTCAACACGAGCTGGCGTCGGAGTAGACGTGCTTGGAGGAGTGGCTGTTGGTGCTGGAGCATGTGGAGTCACTGGCTGGGGTTGTATC[G/A]
ACGAAGAGCTCGTCGTAGTCGAAGTCGTGGCCCGAGGGTGTGTTGGTGTCGGAGTCGGTGGAGATTCGGGGGCTGGGGTAGACACGCTAGGTGAAGAAGA

Reverse complement sequence

TCTTCTTCACCTAGCGTGTCTACCCCAGCCCCCGAATCTCCACCGACTCCGACACCAACACACCCTCGGGCCACGACTTCGACTACGACGAGCTCTTCGT[C/T]
GATACAACCCCAGCCAGTGACTCCACATGCTCCAGCACCAACAGCCACTCCTCCAAGCACGTCTACTCCGACGCCAGCTCGTGTTGAGCGCAGCCCGGTG

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	33.30%	1.90%	16.99%	47.74%	NA
All Indica	2759	6.50%	0.00%	22.40%	71.04%	NA
All Japonica	1512	88.80%	5.90%	3.31%	1.98%	NA
Aus	269	1.50%	0.00%	34.20%	64.31%	NA
Indica I	595	3.40%	0.00%	19.16%	77.48%	NA
Indica II	465	11.80%	0.00%	12.26%	75.91%	NA
Indica III	913	7.30%	0.10%	30.01%	62.54%	NA
Indica Intermediate	786	4.80%	0.00%	22.01%	73.16%	NA
Temperate Japonica	767	86.00%	9.60%	3.52%	0.78%	NA
Tropical Japonica	504	92.30%	1.00%	3.17%	3.57%	NA
Japonica Intermediate	241	90.50%	4.10%	2.90%	2.49%	NA
VI/Aromatic	96	9.40%	0.00%	34.38%	56.25%	NA
Intermediate	90	44.40%	1.10%	11.11%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0217179848	G -> A	LOC_Os02g29030.1	missense_variant ; p.Ser1064Leu; MODERATE	nonsynonymous_codon ; S1064L	Average:32.439; most accessible tissue: Minghui63 young leaf, score: 71.254	unknown	unknown	TOLERATED	0.27
vg0217179848	G -> DEL	LOC_Os02g29030.1	N	frameshift_variant	Average:32.439; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217179848	3.84E-06	6.80E-07	mr1358_2	Jap_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