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Detailed information for vg0217025287:

Variant ID: vg0217025287 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17025287
Reference Allele: T	Alternative Allele: A,C
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTCCTTATACCCGAAAATTGATATTGATGCTGTTGACGGCTCTGCAGACGGGACAAGTGAGGAGGCCGCCCTTGACCTCATCAGTGATGCGCAAAAGGC[T/A,C]
GCTGACAAGATAGCCGCTGATGTAGTTGAGAGATTCCAGGACAACGATCTTAAGCCGACTGGGTCTGATAATTCTGATGATGAAAGAACTGAATCTAATT

Reverse complement sequence

AATTAGATTCAGTTCTTTCATCATCAGAATTATCAGACCCAGTCGGCTTAAGATCGTTGTCCTGGAATCTCTCAACTACATCAGCGGCTATCTTGTCAGC[A/T,G]
GCCTTTTGCGCATCACTGATGAGGTCAAGGGCGGCCTCCTCACTTGTCCCGTCTGCAGAGCCGTCAACAGCATCAATATCAATTTTCGGGTATAAGGACT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.10%	8.90%	1.04%	0.00%	NA
All Indica	2759	96.40%	3.50%	0.07%	0.00%	NA
All Japonica	1512	76.20%	20.80%	3.04%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	92.00%	7.70%	0.22%	0.00%	NA
Indica III	913	95.00%	5.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.00%	1.90%	0.13%	0.00%	NA
Temperate Japonica	767	78.50%	17.10%	4.43%	0.00%	NA
Tropical Japonica	504	86.50%	12.50%	0.99%	0.00%	NA
Japonica Intermediate	241	47.30%	49.80%	2.90%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	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
vg0217025287	T -> A	LOC_Os02g28770.1	synonymous_variant ; p.Ala457Ala; LOW	synonymous_codon	Average:35.928; most accessible tissue: Minghui63 flag leaf, score: 55.781	N	N	N	N
vg0217025287	T -> C	LOC_Os02g28770.1	synonymous_variant ; p.Ala457Ala; LOW	N	Average:35.928; most accessible tissue: Minghui63 flag leaf, score: 55.781	N	N	N	N
vg0217025287	T -> C	LOC_Os02g28780.1	downstream_gene_variant ; 414.0bp to feature; MODIFIER	N	Average:35.928; most accessible tissue: Minghui63 flag leaf, score: 55.781	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217025287	4.65E-06	NA	mr1093	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
vg0217025287	8.46E-06	8.46E-06	mr1914	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
vg0217025287	NA	1.65E-06	mr1187_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
vg0217025287	NA	3.30E-06	mr1240_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
vg0217025287	4.66E-10	NA	mr1317_2	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
vg0217025287	2.87E-07	2.87E-07	mr1317_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
vg0217025287	NA	2.02E-06	mr1496_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
vg0217025287	NA	2.05E-08	mr1691_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
vg0217025287	9.21E-09	NA	mr1897_2	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
vg0217025287	8.35E-07	8.35E-07	mr1897_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
vg0217025287	2.19E-09	NA	mr1914_2	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
vg0217025287	1.26E-09	1.26E-09	mr1914_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
vg0217025287	1.97E-07	NA	mr1927_2	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
vg0217025287	5.19E-07	5.19E-07	mr1927_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