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Detailed information for vg0716738061:

Variant ID: vg0716738061 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16738061
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGCCCGAGCTAATTCGAAACTTTCATATATACCTTCTCGTAGGAAACGGCACCACGGCAATCAAAACGGCAGCCGAAGAAAAAAGTTCCGTCGAAAGAC[G/A]
ACGAGGCACCAACTAACACAACCGGCTCAAACAAAAGCGAACGGTCAGCAAAGGCGAAGAAAAGGAAGGGCGAGAGAAGCGTGAATAAAAAGGATGAAGG

Reverse complement sequence

CCTTCATCCTTTTTATTCACGCTTCTCTCGCCCTTCCTTTTCTTCGCCTTTGCTGACCGTTCGCTTTTGTTTGAGCCGGTTGTGTTAGTTGGTGCCTCGT[C/T]
GTCTTTCGACGGAACTTTTTTCTTCGGCTGCCGTTTTGATTGCCGTGGTGCCGTTTCCTACGAGAAGGTATATATGAAAGTTTCGAATTAGCTCGGGCTA

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	71.60%	8.10%	17.71%	2.52%	NA
All Indica	2759	72.80%	0.20%	23.92%	3.12%	NA
All Japonica	1512	70.00%	24.00%	5.82%	0.20%	NA
Aus	269	63.60%	0.00%	26.02%	10.41%	NA
Indica I	595	79.70%	0.00%	17.48%	2.86%	NA
Indica II	465	73.50%	0.20%	21.72%	4.52%	NA
Indica III	913	66.80%	0.40%	31.54%	1.20%	NA
Indica Intermediate	786	74.00%	0.00%	21.25%	4.71%	NA
Temperate Japonica	767	91.30%	2.00%	6.39%	0.39%	NA
Tropical Japonica	504	41.90%	53.80%	4.37%	0.00%	NA
Japonica Intermediate	241	61.00%	32.00%	7.05%	0.00%	NA
VI/Aromatic	96	92.70%	4.20%	3.12%	0.00%	NA
Intermediate	90	65.60%	14.40%	17.78%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0716738061	G -> DEL	LOC_Os07g28600.1	N	frameshift_variant	Average:21.629; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0716738061	G -> A	LOC_Os07g28600.1	missense_variant ; p.Asp100Asn; MODERATE	nonsynonymous_codon ; D100N	Average:21.629; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	benign	0.403	TOLERATED	0.06

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716738061	3.23E-06	NA	mr1082	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
vg0716738061	NA	1.67E-06	mr1082	Jap_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
vg0716738061	2.75E-06	NA	mr1083	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
vg0716738061	6.93E-07	NA	mr1085	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
vg0716738061	3.35E-07	NA	mr1226	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
vg0716738061	NA	1.16E-08	mr1408	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
vg0716738061	NA	8.95E-06	mr1852	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
vg0716738061	NA	1.11E-06	mr1063_2	Jap_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
vg0716738061	NA	2.11E-07	mr1183_2	Jap_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
vg0716738061	2.83E-06	NA	mr1226_2	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
vg0716738061	NA	5.09E-07	mr1408_2	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
vg0716738061	NA	5.44E-06	mr1556_2	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
vg0716738061	NA	1.18E-06	mr1966_2	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