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Detailed information for vg0613084325:

Variant ID: vg0613084325 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13084325
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCTGAACGGCCATGGCTTAATAATAGGATTCATAGCCAACGTCGGCGCTCGCTGAATTGCTCCAAACTTTTGACAATCTTGACACCCCCTATAATATCT[G/A]
AAACAATCCTCCAGCATTGTCGGCCAAAAGTACCCTGCACGCAGAAGCAACCACTTCATCTTATGAGCCGATTGATGAGTACCACAGATTCCTTCATGAA

Reverse complement sequence

TTCATGAAGGAATCTGTGGTACTCATCAATCGGCTCATAAGATGAAGTGGTTGCTTCTGCGTGCAGGGTACTTTTGGCCGACAATGCTGGAGGATTGTTT[C/T]
AGATATTATAGGGGGTGTCAAGATTGTCAAAAGTTTGGAGCAATTCAGCGAGCGCCGACGTTGGCTATGAATCCTATTATTAAGCCATGGCCGTTCAGAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.70%	38.70%	1.42%	0.19%	NA
All Indica	2759	93.40%	3.90%	2.36%	0.33%	NA
All Japonica	1512	3.00%	97.00%	0.00%	0.00%	NA
Aus	269	57.60%	42.00%	0.37%	0.00%	NA
Indica I	595	90.60%	3.70%	4.54%	1.18%	NA
Indica II	465	92.00%	4.90%	2.80%	0.22%	NA
Indica III	913	98.20%	1.60%	0.11%	0.00%	NA
Indica Intermediate	786	90.80%	6.00%	3.05%	0.13%	NA
Temperate Japonica	767	3.50%	96.50%	0.00%	0.00%	NA
Tropical Japonica	504	3.00%	97.00%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	3.10%	96.90%	0.00%	0.00%	NA
Intermediate	90	44.40%	54.40%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0613084325	G -> A	LOC_Os06g22520.1	synonymous_variant ; p.Phe1505Phe; LOW	synonymous_codon	Average:32.021; most accessible tissue: Minghui63 young leaf, score: 43.347	N	N	N	N
vg0613084325	G -> DEL	LOC_Os06g22520.1	N	frameshift_variant	Average:32.021; most accessible tissue: Minghui63 young leaf, score: 43.347	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613084325	NA	7.61E-10	mr1033	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
vg0613084325	NA	7.46E-26	mr1076	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
vg0613084325	NA	1.90E-07	mr1076	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
vg0613084325	NA	1.22E-38	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
vg0613084325	NA	1.59E-06	mr1082	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
vg0613084325	NA	1.43E-06	mr1085	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
vg0613084325	NA	3.74E-06	mr1103	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
vg0613084325	NA	9.63E-07	mr1176	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
vg0613084325	NA	5.11E-06	mr1204	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
vg0613084325	NA	4.99E-42	mr1534	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
vg0613084325	NA	5.98E-08	mr1560	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
vg0613084325	NA	6.37E-07	mr1620	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
vg0613084325	NA	1.88E-13	mr1713	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
vg0613084325	7.90E-07	4.20E-69	mr1865	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