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Detailed information for vg0320737151:

Variant ID: vg0320737151 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20737151
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGGACGTGCAGCAACTCTTCAGATACGAGTTGAACCACACCTCACGACCCCGGAGTGTCTCTACAGCCTGGTCCTTCTTCACTTCCAGCATAGTCCTCT[C/T]
GAGTTCCGCGACCTCAAACTTCGTCCTCCAATAATGGATGCGACGATCCTGGTCAGCGAGCGCGCTCTCGAGGTCTACGCAGCATGGAAACGATTAAGTT

Reverse complement sequence

AACTTAATCGTTTCCATGCTGCGTAGACCTCGAGAGCGCGCTCGCTGACCAGGATCGTCGCATCCATTATTGGAGGACGAAGTTTGAGGTCGCGGAACTC[G/A]
AGAGGACTATGCTGGAAGTGAAGAAGGACCAGGCTGTAGAGACACTCCGGGGTCGTGAGGTGTGGTTCAACTCGTATCTGAAGAGTTGCTGCACGTCCAT

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	46.30%	1.50%	6.16%	46.09%	NA
All Indica	2759	17.70%	2.50%	8.08%	71.73%	NA
All Japonica	1512	95.20%	0.00%	1.19%	3.57%	NA
Aus	269	40.90%	0.40%	14.87%	43.87%	NA
Indica I	595	8.90%	0.80%	2.35%	87.90%	NA
Indica II	465	29.70%	2.60%	11.18%	56.56%	NA
Indica III	913	15.90%	2.60%	10.08%	71.41%	NA
Indica Intermediate	786	19.30%	3.60%	8.27%	68.83%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	88.30%	0.00%	2.98%	8.73%	NA
Japonica Intermediate	241	95.00%	0.00%	1.24%	3.73%	NA
VI/Aromatic	96	87.50%	0.00%	7.29%	5.21%	NA
Intermediate	90	71.10%	1.10%	3.33%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0320737151	C -> T	LOC_Os03g37411.1	intron_variant ; MODIFIER	silent_mutation	Average:18.894; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0320737151	C -> DEL	N	N	silent_mutation	Average:18.894; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320737151	5.79E-06	NA	mr1682	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
vg0320737151	2.86E-06	NA	mr1754	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