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Detailed information for vg0221753297:

Variant ID: vg0221753297 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21753297
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAAAAACCGAAAAAAAAACAAGAGAAAAAACGAGGAAAAAACCGCCACACGTGGCCTCCCGCACCGTTCCACCGCCACTCCCCCTCTCCGCGTGCGCCA[C/T]
GTGGTTGCACCGAGTGGGTAGGGGAGCGGGGTAAGGGAGCGCGTGACTGATCGCCTTTTAGTGATCTCGCCATCCACCCCCAAACCTGAGAAAGAGATAA

Reverse complement sequence

TTATCTCTTTCTCAGGTTTGGGGGTGGATGGCGAGATCACTAAAAGGCGATCAGTCACGCGCTCCCTTACCCCGCTCCCCTACCCACTCGGTGCAACCAC[G/A]
TGGCGCACGCGGAGAGGGGGAGTGGCGGTGGAACGGTGCGGGAGGCCACGTGTGGCGGTTTTTTCCTCGTTTTTTCTCTTGTTTTTTTTTCGGTTTTTTC

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	93.40%	6.20%	0.44%	0.00%	NA
All Indica	2759	99.60%	0.40%	0.04%	0.00%	NA
All Japonica	1512	80.50%	18.30%	1.26%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.70%	1.20%	0.17%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	67.40%	30.40%	2.22%	0.00%	NA
Tropical Japonica	504	98.00%	1.80%	0.20%	0.00%	NA
Japonica Intermediate	241	85.50%	14.10%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	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
vg0221753297	C -> T	LOC_Os02g36130-LOC_Os02g36140	intergenic_region ; MODIFIER	silent_mutation	Average:61.939; most accessible tissue: Callus, score: 83.223	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221753297	NA	9.98E-06	mr1858	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
vg0221753297	1.61E-06	1.61E-06	mr1868	Jap_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
vg0221753297	NA	6.87E-06	mr1164_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