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Detailed information for vg0203405625:

Variant ID: vg0203405625 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 3405625
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTCTGTCCAGTGCCAGCGCATGTGCCATGCTTTCATAGGTCATAGACTGCCCTCACAGACCAACACATGTCTTTTCTGCACACTTTGTCCTCACTCGTG[C/T]
GCACCCGGGAAGAATTTCTCGGTCGGTCACCCATCCCAAATTGCTCCAGGCCAAACACGCTTAACCCTGGAGTTCTTTGGAGATCGGTTTCCAGAAAAGA

Reverse complement sequence

TCTTTTCTGGAAACCGATCTCCAAAGAACTCCAGGGTTAAGCGTGTTTGGCCTGGAGCAATTTGGGATGGGTGACCGACCGAGAAATTCTTCCCGGGTGC[G/A]
CACGAGTGAGGACAAAGTGTGCAGAAAAGACATGTGTTGGTCTGTGAGGGCAGTCTATGACCTATGAAAGCATGGCACATGCGCTGGCACTGGACAGACG

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	35.30%	1.20%	2.41%	61.15%	NA
All Indica	2759	16.10%	1.30%	3.62%	79.05%	NA
All Japonica	1512	62.50%	0.10%	0.53%	36.90%	NA
Aus	269	82.50%	6.30%	0.74%	10.41%	NA
Indica I	595	17.80%	0.00%	3.53%	78.66%	NA
Indica II	465	13.30%	0.00%	6.24%	80.43%	NA
Indica III	913	14.70%	3.50%	2.08%	79.74%	NA
Indica Intermediate	786	17.90%	0.40%	3.94%	77.74%	NA
Temperate Japonica	767	72.00%	0.00%	0.52%	27.51%	NA
Tropical Japonica	504	55.80%	0.00%	0.20%	44.05%	NA
Japonica Intermediate	241	46.50%	0.40%	1.24%	51.87%	NA
VI/Aromatic	96	13.50%	0.00%	3.12%	83.33%	NA
Intermediate	90	48.90%	2.20%	1.11%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0203405625	C -> T	LOC_Os02g06754.1	upstream_gene_variant ; 2399.0bp to feature; MODIFIER	silent_mutation	Average:15.767; most accessible tissue: Minghui63 young leaf, score: 26.082	N	N	N	N
vg0203405625	C -> T	LOC_Os02g06750.1	intron_variant ; MODIFIER	silent_mutation	Average:15.767; most accessible tissue: Minghui63 young leaf, score: 26.082	N	N	N	N
vg0203405625	C -> DEL	N	N	silent_mutation	Average:15.767; most accessible tissue: Minghui63 young leaf, score: 26.082	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203405625	7.13E-10	9.30E-14	mr1514_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
vg0203405625	2.65E-09	9.70E-10	mr1514_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