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Detailed information for vg0320151239:

Variant ID: vg0320151239 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20151239
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGAGCTGGAGAAGAGATGCGGATGGGCGGCCTTCAACTCATCTTCCCTTTCCCAGGTTGCCTTTTCCTCTGAATGGTGGCTCCACTGAACCCTGGAGAG[T/C]
CTAGTGACCTTGTTTCTGGTTCTTCTTTCACTGGTCTCAAGGATGCGAACTGGCTTCTCCACGTAGGTCAGATCCTCTTGGATATCGATGTGCTCCGAAT

Reverse complement sequence

ATTCGGAGCACATCGATATCCAAGAGGATCTGACCTACGTGGAGAAGCCAGTTCGCATCCTTGAGACCAGTGAAAGAAGAACCAGAAACAAGGTCACTAG[A/G]
CTCTCCAGGGTTCAGTGGAGCCACCATTCAGAGGAAAAGGCAACCTGGGAAAGGGAAGATGAGTTGAAGGCCGCCCATCCGCATCTCTTCTCCAGCTCCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.80%	37.50%	2.31%	2.35%	NA
All Indica	2759	84.10%	11.50%	2.57%	1.92%	NA
All Japonica	1512	11.70%	86.70%	0.20%	1.39%	NA
Aus	269	65.10%	10.00%	11.90%	13.01%	NA
Indica I	595	57.50%	33.30%	6.72%	2.52%	NA
Indica II	465	93.10%	5.60%	0.43%	0.86%	NA
Indica III	913	96.10%	1.30%	0.33%	2.30%	NA
Indica Intermediate	786	84.90%	10.20%	3.31%	1.65%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	31.20%	68.30%	0.20%	0.40%	NA
Japonica Intermediate	241	7.50%	83.80%	0.83%	7.88%	NA
VI/Aromatic	96	25.00%	75.00%	0.00%	0.00%	NA
Intermediate	90	42.20%	52.20%	3.33%	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
vg0320151239	T -> C	LOC_Os03g36330.1	synonymous_variant ; p.Arg719Arg; LOW	synonymous_codon	Average:25.377; most accessible tissue: Minghui63 young leaf, score: 50.756	N	N	N	N
vg0320151239	T -> DEL	LOC_Os03g36330.1	N	frameshift_variant	Average:25.377; most accessible tissue: Minghui63 young leaf, score: 50.756	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320151239	NA	1.73E-07	mr1136	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
vg0320151239	NA	4.49E-11	mr1188	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
vg0320151239	NA	4.62E-07	mr1227	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
vg0320151239	NA	9.82E-09	mr1718	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
vg0320151239	7.14E-06	NA	mr1750	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
vg0320151239	3.62E-09	3.45E-18	mr1750	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
vg0320151239	NA	6.70E-07	mr1845	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
vg0320151239	1.79E-06	1.79E-06	mr1987	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
vg0320151239	NA	2.78E-11	mr1188_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
vg0320151239	NA	5.04E-07	mr1188_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
vg0320151239	NA	9.56E-13	mr1217_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
vg0320151239	NA	5.99E-15	mr1718_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
vg0320151239	NA	3.67E-11	mr1722_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
vg0320151239	3.56E-06	NA	mr1750_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
vg0320151239	8.36E-11	1.76E-23	mr1750_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
vg0320151239	NA	1.35E-07	mr1987_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