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Detailed information for vg0210480404:

Variant ID: vg0210480404 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10480404
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGAAGGAGACTCTCAAGAAGGCTTTTGATCAAGTCTACGCCGCATTTGAGCCGCTAAGCGATGTAGATGGTGATAGTGGCGATGAAGATAAGGGAAAGAA[C/T]
ATCTCCGGTGTTTGCTTCATGGCGCGTGGTGAATCGGATTCATAGTGTGAAGACAATGAAGTACGTGTTTTTGAGGAAGCTATTCTTATTTTAAGTGAGA

Reverse complement sequence

TCTCACTTAAAATAAGAATAGCTTCCTCAAAAACACGTACTTCATTGTCTTCACACTATGAATCCGATTCACCACGCGCCATGAAGCAAACACCGGAGAT[G/A]
TTCTTTCCCTTATCTTCATCGCCACTATCACCATCTACATCGCTTAGCGGCTCAAATGCGGCGTAGACTTGATCAAAAGCCTTCTTGAGAGTCTCCTTCA

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	87.70%	0.50%	6.47%	5.29%	NA
All Indica	2759	82.20%	0.90%	9.82%	7.10%	NA
All Japonica	1512	99.50%	0.00%	0.20%	0.26%	NA
Aus	269	73.20%	0.40%	9.29%	17.10%	NA
Indica I	595	74.80%	0.70%	13.78%	10.76%	NA
Indica II	465	82.60%	0.90%	9.03%	7.53%	NA
Indica III	913	87.40%	1.10%	7.78%	3.72%	NA
Indica Intermediate	786	81.60%	0.80%	9.67%	8.02%	NA
Temperate Japonica	767	99.60%	0.00%	0.13%	0.26%	NA
Tropical Japonica	504	99.40%	0.00%	0.20%	0.40%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	0.00%	7.78%	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
vg0210480404	C -> T	LOC_Os02g18050.1	synonymous_variant ; p.Asn108Asn; LOW	synonymous_codon	Average:22.026; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N
vg0210480404	C -> DEL	LOC_Os02g18050.1	N	frameshift_variant	Average:22.026; most accessible tissue: Zhenshan97 root, score: 39.742	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210480404	NA	2.73E-07	mr1129_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
vg0210480404	5.80E-07	NA	mr1255_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
vg0210480404	1.18E-06	4.42E-08	mr1255_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