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Detailed information for vg0615048049:

Variant ID: vg0615048049 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 15048049
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCAATCGGCTAAGGCAGACAAGAGTTTCTGTTCATCAAAGATTGGGTCCAGTAAATCAAGATCATGGCCAAGAGGACAATGTAATCAGGAAGAATCAAT[G/C]
GTGTCCTTCTAGTATTTTCACGAAGAATCAGAAGAGAAGGGTTCAGAGATTGAGGAACAGGGAGCACCTTCAGGAGGTTGAACAAGAAATTAATCATCGG

Reverse complement sequence

CCGATGATTAATTTCTTGTTCAACCTCCTGAAGGTGCTCCCTGTTCCTCAATCTCTGAACCCTTCTCTTCTGATTCTTCGTGAAAATACTAGAAGGACAC[C/G]
ATTGATTCTTCCTGATTACATTGTCCTCTTGGCCATGATCTTGATTTACTGGACCCAATCTTTGATGAACAGAAACTCTTGTCTGCCTTAGCCGATTGCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.40%	32.30%	0.68%	0.68%	NA
All Indica	2759	96.60%	3.20%	0.18%	0.04%	NA
All Japonica	1512	8.90%	91.00%	0.07%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	93.90%	5.50%	0.50%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	99.20%	0.70%	0.11%	0.00%	NA
Indica Intermediate	786	94.40%	5.30%	0.13%	0.13%	NA
Temperate Japonica	767	3.70%	96.30%	0.00%	0.00%	NA
Tropical Japonica	504	17.70%	82.30%	0.00%	0.00%	NA
Japonica Intermediate	241	7.50%	92.10%	0.41%	0.00%	NA
VI/Aromatic	96	20.80%	22.90%	23.96%	32.29%	NA
Intermediate	90	57.80%	38.90%	3.33%	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
vg0615048049	G -> C	LOC_Os06g25760.1	missense_variant ; p.Trp531Ser; MODERATE	nonsynonymous_codon ; W531S	Average:25.243; most accessible tissue: Minghui63 panicle, score: 53.77	probably damaging	2.27	DELETERIOUS	0.00
vg0615048049	G -> DEL	LOC_Os06g25760.1	N	frameshift_variant	Average:25.243; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0615048049	NA	1.82E-23	mr1020	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
vg0615048049	NA	2.80E-06	mr1020	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
vg0615048049	NA	4.26E-19	mr1021	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
vg0615048049	NA	2.20E-16	mr1032	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
vg0615048049	3.22E-07	3.22E-07	mr1032	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
vg0615048049	NA	4.15E-12	mr1033	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
vg0615048049	NA	4.85E-18	mr1165	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
vg0615048049	NA	2.72E-20	mr1477	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
vg0615048049	NA	3.76E-17	mr1478	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
vg0615048049	1.17E-07	1.17E-07	mr1478	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
vg0615048049	4.79E-07	4.79E-07	mr1536	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
vg0615048049	NA	2.47E-22	mr1971	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
vg0615048049	NA	1.28E-07	mr1971	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
vg0615048049	NA	6.20E-16	mr1033_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
vg0615048049	NA	4.94E-09	mr1536_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