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Detailed information for vg0716554289:

Variant ID: vg0716554289 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16554289
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACCATCACGCCCACCCTTGCCTGGATGCGTCAACTAGAGGAAAGCTACACTACAAGCCCAGCCGTTGCCCACGCTAGCTTGTGGTAAGTACGAGGAATT[G/C]
TTCTAGGGTTTCCCGCGAACCGGTCCTCAAGTGCCATGGGCGCGACCATCACAACCATGCACCCACAGCCCACTAGATGGTATATTTTAATTGACTAACA

Reverse complement sequence

TGTTAGTCAATTAAAATATACCATCTAGTGGGCTGTGGGTGCATGGTTGTGATGGTCGCGCCCATGGCACTTGAGGACCGGTTCGCGGGAAACCCTAGAA[C/G]
AATTCCTCGTACTTACCACAAGCTAGCGTGGGCAACGGCTGGGCTTGTAGTGTAGCTTTCCTCTAGTTGACGCATCCAGGCAAGGGTGGGCGTGATGGTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.00%	7.40%	8.74%	39.89%	NA
All Indica	2759	25.10%	1.90%	12.03%	60.93%	NA
All Japonica	1512	80.40%	18.30%	0.73%	0.60%	NA
Aus	269	15.60%	4.50%	20.82%	59.11%	NA
Indica I	595	45.20%	0.20%	5.38%	49.24%	NA
Indica II	465	7.30%	0.40%	9.46%	82.80%	NA
Indica III	913	19.20%	0.80%	18.18%	61.88%	NA
Indica Intermediate	786	27.40%	5.50%	11.45%	55.73%	NA
Temperate Japonica	767	93.90%	4.60%	0.91%	0.65%	NA
Tropical Japonica	504	56.70%	42.50%	0.60%	0.20%	NA
Japonica Intermediate	241	87.10%	11.20%	0.41%	1.24%	NA
VI/Aromatic	96	85.40%	0.00%	11.46%	3.12%	NA
Intermediate	90	50.00%	10.00%	3.33%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0716554289	G -> DEL	N	N	silent_mutation	Average:36.945; most accessible tissue: Zhenshan97 flag leaf, score: 82.529	N	N	N	N
vg0716554289	G -> C	LOC_Os07g28350.1	downstream_gene_variant ; 4310.0bp to feature; MODIFIER	silent_mutation	Average:36.945; most accessible tissue: Zhenshan97 flag leaf, score: 82.529	N	N	N	N
vg0716554289	G -> C	LOC_Os07g28360.1	intron_variant ; MODIFIER	silent_mutation	Average:36.945; most accessible tissue: Zhenshan97 flag leaf, score: 82.529	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716554289	1.62E-07	NA	mr1705_2	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
vg0716554289	1.59E-06	7.34E-10	mr1705_2	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