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Detailed information for vg0200471574:

Variant ID: vg0200471574 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 471574
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCGCCGCAGACGCCACCGGCTTCGCCGTAGACGCCGCCGCCACAGCCGCCACCACCACGCTCACGCCACTCTCCCTCTCTGGCACTACTGACCTTGTG[C/T]
GCATCGGCGCCGCTGAAGAGGAGGAGCCGCAAGCAGGCTCCGCCGCCGGCTCCGCCCGCCGCCGACTCCGCCACCGCCGCCGGCTCCGCCGCCGCAGCCA

Reverse complement sequence

TGGCTGCGGCGGCGGAGCCGGCGGCGGTGGCGGAGTCGGCGGCGGGCGGAGCCGGCGGCGGAGCCTGCTTGCGGCTCCTCCTCTTCAGCGGCGCCGATGC[G/A]
CACAAGGTCAGTAGTGCCAGAGAGGGAGAGTGGCGTGAGCGTGGTGGTGGCGGCTGTGGCGGCGGCGTCTACGGCGAAGCCGGTGGCGTCTGCGGCGGAG

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	83.50%	7.20%	6.45%	2.84%	NA
All Indica	2759	82.60%	12.20%	3.37%	1.85%	NA
All Japonica	1512	81.40%	0.00%	13.49%	5.09%	NA
Aus	269	97.80%	0.00%	0.74%	1.49%	NA
Indica I	595	98.50%	0.80%	0.50%	0.17%	NA
Indica II	465	84.30%	8.00%	4.95%	2.80%	NA
Indica III	913	72.60%	20.40%	4.49%	2.52%	NA
Indica Intermediate	786	81.20%	13.70%	3.31%	1.78%	NA
Temperate Japonica	767	75.00%	0.00%	19.95%	5.08%	NA
Tropical Japonica	504	90.30%	0.00%	4.37%	5.36%	NA
Japonica Intermediate	241	83.40%	0.00%	12.03%	4.56%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	88.90%	4.40%	4.44%	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
vg0200471574	C -> T	LOC_Os02g01850.1	synonymous_variant ; p.Ala34Ala; LOW	synonymous_codon	Average:67.177; most accessible tissue: Minghui63 panicle, score: 93.294	N	N	N	N
vg0200471574	C -> DEL	LOC_Os02g01850.1	N	frameshift_variant	Average:67.177; most accessible tissue: Minghui63 panicle, score: 93.294	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0200471574	NA	9.80E-06	mr1075	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
vg0200471574	NA	5.44E-06	mr1124	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
vg0200471574	NA	6.13E-07	mr1457	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
vg0200471574	NA	4.72E-09	mr1458	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
vg0200471574	NA	8.69E-06	mr1074_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
vg0200471574	5.75E-06	5.75E-06	mr1081_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
vg0200471574	NA	9.33E-06	mr1711_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
vg0200471574	NA	3.68E-06	mr1743_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
vg0200471574	2.53E-06	1.94E-07	mr1790_2	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
vg0200471574	2.95E-06	5.47E-07	mr1805_2	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
vg0200471574	NA	9.55E-06	mr1943_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