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Detailed information for vg0719728074:

Variant ID: vg0719728074 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 19728074
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCAGGAACAATTGAGCACTCGGGTAGGTTATGGTCGAGTACACTCCATTATCGAGAACATTCTCGACAAATGCGGAGTTATCGCACCCAACCTACCAAC[G/A]
AAGACCGATGACCTATCTCATAGCACCGGCCATCGCTGGACTACTCGAGAAAAGGTTGTTAACAGATAATTCCTGGCGAACGCCGTTGGCTTGATCACCC

Reverse complement sequence

GGGTGATCAAGCCAACGGCGTTCGCCAGGAATTATCTGTTAACAACCTTTTCTCGAGTAGTCCAGCGATGGCCGGTGCTATGAGATAGGTCATCGGTCTT[C/T]
GTTGGTAGGTTGGGTGCGATAACTCCGCATTTGTCGAGAATGTTCTCGATAATGGAGTGTACTCGACCATAACCTACCCGAGTGCTCAATTGTTCCTGAA

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	54.20%	0.60%	5.42%	39.78%	NA
All Indica	2759	29.90%	0.40%	7.43%	62.27%	NA
All Japonica	1512	97.90%	1.00%	0.33%	0.79%	NA
Aus	269	48.30%	0.40%	9.67%	41.64%	NA
Indica I	595	23.50%	0.20%	9.92%	66.39%	NA
Indica II	465	32.30%	0.00%	6.24%	61.51%	NA
Indica III	913	29.70%	0.40%	7.12%	62.76%	NA
Indica Intermediate	786	33.60%	0.80%	6.62%	59.03%	NA
Temperate Japonica	767	96.50%	2.00%	0.39%	1.17%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	0.00%	0.83%	1.24%	NA
VI/Aromatic	96	76.00%	0.00%	17.71%	6.25%	NA
Intermediate	90	61.10%	0.00%	3.33%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0719728074	G -> DEL	LOC_Os07g33020.1	N	frameshift_variant	Average:14.096; most accessible tissue: Callus, score: 24.996	N	N	N	N
vg0719728074	G -> A	LOC_Os07g33020.1	synonymous_variant ; p.Thr80Thr; LOW	synonymous_codon	Average:14.096; most accessible tissue: Callus, score: 24.996	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0719728074	4.67E-07	4.39E-06	mr1120	Ind_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