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Detailed information for vg0714405943:

Variant ID: vg0714405943 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14405943
Reference Allele: G	Alternative Allele: A,C
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: 39. )

Flanking Sequence (100 bp) in Reference Genome:

TGACCTTTCTTTTACGGTTCATTTTGTTACACTGCTCCTCCTGATGGATAGCCTTGTCCACAAGCTTCTCAAAGTCCTCATAGTCTCTGGAGATCAGCTG[G/A,C]
TTGGTCAATTCATCATCAAGACCAAACAAAAACTTCTCCTGCTTCTCAGCATCAGTGCGCACGTCCTCAGGAGCATAGCGCGCGAGGCGGTTGAACTCAT

Reverse complement sequence

ATGAGTTCAACCGCCTCGCGCGCTATGCTCCTGAGGACGTGCGCACTGATGCTGAGAAGCAGGAGAAGTTTTTGTTTGGTCTTGATGATGAATTGACCAA[C/T,G]
CAGCTGATCTCCAGAGACTATGAGGACTTTGAGAAGCTTGTGGACAAGGCTATCCATCAGGAGGAGCAGTGTAACAAAATGAACCGTAAAAGAAAGGTCA

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	47.20%	0.90%	1.86%	49.98%	C: 0.02%
All Indica	2759	27.10%	1.50%	2.65%	68.76%	C: 0.04%
All Japonica	1512	84.50%	0.00%	0.46%	15.01%	NA
Aus	269	23.80%	0.70%	2.23%	73.23%	NA
Indica I	595	52.40%	1.80%	2.18%	43.53%	NA
Indica II	465	31.00%	1.70%	2.37%	64.95%	NA
Indica III	913	5.40%	1.40%	2.74%	90.47%	NA
Indica Intermediate	786	30.80%	1.10%	3.05%	64.89%	C: 0.13%
Temperate Japonica	767	85.00%	0.00%	0.65%	14.34%	NA
Tropical Japonica	504	94.00%	0.00%	0.20%	5.75%	NA
Japonica Intermediate	241	63.10%	0.00%	0.41%	36.51%	NA
VI/Aromatic	96	85.40%	0.00%	0.00%	14.58%	NA
Intermediate	90	66.70%	1.10%	2.22%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714405943	G -> DEL	LOC_Os07g25210.1	N	frameshift_variant	Average:14.752; most accessible tissue: Callus, score: 45.109	N	N	N	N
vg0714405943	G -> A	LOC_Os07g25210.1	synonymous_variant ; p.Asn629Asn; LOW	synonymous_codon	Average:14.752; most accessible tissue: Callus, score: 45.109	N	N	N	N
vg0714405943	G -> C	LOC_Os07g25210.1	missense_variant ; p.Asn629Lys; MODERATE	nonsynonymous_codon	Average:14.752; most accessible tissue: Callus, score: 45.109	possibly damaging	1.504	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714405943	3.85E-06	NA	mr1632	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