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Detailed information for vg0721354156:

Variant ID: vg0721354156 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 21354156
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTATATTACAAGTCGTTTTAACTTTTTCTCTACTCAAATTTCTTTAGCTTTGATCAAGTGTATAAAATTTAGTAACATCGACAACACCAAATTAGTTT[C/T]
ATTACTTGTAGCATTGAATACATTTTGTTAATATGTTTGTTTTGGGTCAAAAATATCGTTATATTATCTACAAATTTTATCAAACTAAAAAATGATTAGT

Reverse complement sequence

ACTAATCATTTTTTAGTTTGATAAAATTTGTAGATAATATAACGATATTTTTGACCCAAAACAAACATATTAACAAAATGTATTCAATGCTACAAGTAAT[G/A]
AAACTAATTTGGTGTTGTCGATGTTACTAAATTTTATACACTTGATCAAAGCTAAAGAAATTTGAGTAGAGAAAAAGTTAAAACGACTTGTAATATAAAA

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	93.80%	6.20%	0.02%	0.00%	NA
All Indica	2759	98.70%	1.30%	0.00%	0.00%	NA
All Japonica	1512	83.50%	16.50%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	95.70%	4.30%	0.00%	0.00%	NA
Temperate Japonica	767	79.00%	21.00%	0.00%	0.00%	NA
Tropical Japonica	504	96.20%	3.80%	0.00%	0.00%	NA
Japonica Intermediate	241	71.40%	28.60%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	95.60%	3.30%	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
vg0721354156	C -> T	LOC_Os07g35650.1	intron_variant ; MODIFIER	silent_mutation	Average:22.076; most accessible tissue: Callus, score: 41.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0721354156	2.12E-06	NA	mr1019_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
vg0721354156	8.48E-07	NA	mr1531_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
vg0721354156	NA	6.45E-06	mr1531_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