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Detailed information for vg0621526127:

Variant ID: vg0621526127 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 21526127
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCATTGTAGGAAGGTTGTGTACATGGGTCATTGTCGATTCCTTGCTGCAAACCACCCGGTACGGAAGAAAGGCAAGCACTTTGAACATAAGGCGGACCA[C/T]
TGTACGAAGCCTAAATATCGTAGTGGGAAAACAGTGTTTGCTATGGTTAAAGATTTTAAAGTAGTGTTCGGAAAGGGGCCTGGAAGCCAGCCTACAGAGA

Reverse complement sequence

TCTCTGTAGGCTGGCTTCCAGGCCCCTTTCCGAACACTACTTTAAAATCTTTAACCATAGCAAACACTGTTTTCCCACTACGATATTTAGGCTTCGTACA[G/A]
TGGTCCGCCTTATGTTCAAAGTGCTTGCCTTTCTTCCGTACCGGGTGGTTTGCAGCAAGGAATCGACAATGACCCATGTACACAACCTTCCTACAATGCT

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	88.20%	0.30%	4.27%	7.28%	NA
All Indica	2759	81.30%	0.40%	6.89%	11.45%	NA
All Japonica	1512	97.90%	0.10%	0.60%	1.39%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	93.40%	0.70%	2.69%	3.19%	NA
Indica II	465	93.80%	0.20%	4.09%	1.94%	NA
Indica III	913	66.80%	0.10%	12.05%	21.03%	NA
Indica Intermediate	786	81.60%	0.50%	5.73%	12.21%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	94.20%	0.20%	1.59%	3.97%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	NA
Intermediate	90	92.20%	0.00%	3.33%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0621526127	C -> T	LOC_Os06g36640.1	synonymous_variant ; p.His359His; LOW	synonymous_codon	Average:31.818; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0621526127	C -> DEL	LOC_Os06g36640.1	N	frameshift_variant	Average:31.818; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0621526127	NA	1.01E-06	mr1583	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
vg0621526127	NA	7.42E-08	mr1648	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
vg0621526127	NA	2.86E-06	mr1215_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
vg0621526127	NA	6.27E-06	mr1566_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
vg0621526127	NA	2.80E-08	mr1583_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