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Detailed information for vg0722147042:

Variant ID: vg0722147042 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 22147042
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTAATACTATGTAATTATGCGAGTTTAGGAGAAGCATCCACATATGGTCATGTATAGGAGATGTAGGCCCTGTTTAGTTCCTAAAATAAAAATTTTCACG[T/C]
TGTCACATTGAATGTTTTGGCATATACATAGAGTATTAAATATAGGGAAAAAAAACCAATTTCACAGACTGCGTGTAAATTGCGAGAGGAATCTTTTAAG

Reverse complement sequence

CTTAAAAGATTCCTCTCGCAATTTACACGCAGTCTGTGAAATTGGTTTTTTTTCCCTATATTTAATACTCTATGTATATGCCAAAACATTCAATGTGACA[A/G]
CGTGAAAATTTTTATTTTAGGAACTAAACAGGGCCTACATCTCCTATACATGACCATATGTGGATGCTTCTCCTAAACTCGCATAATTACATAGTATTAG

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	89.40%	8.30%	2.26%	0.00%	NA
All Indica	2759	99.20%	0.70%	0.14%	0.00%	NA
All Japonica	1512	69.60%	23.80%	6.55%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.60%	2.20%	0.22%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	0.90%	0.38%	0.00%	NA
Temperate Japonica	767	47.20%	42.80%	10.04%	0.00%	NA
Tropical Japonica	504	95.80%	2.60%	1.59%	0.00%	NA
Japonica Intermediate	241	86.30%	7.90%	5.81%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	81.10%	15.60%	3.33%	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
vg0722147042	T -> C	LOC_Os07g36980-LOC_Os07g36990	intergenic_region ; MODIFIER	silent_mutation	Average:31.309; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0722147042	NA	5.07E-06	mr1977	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
vg0722147042	NA	5.42E-06	mr1910_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
vg0722147042	5.94E-06	5.00E-10	mr1946_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
vg0722147042	5.94E-06	5.00E-10	mr1948_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
vg0722147042	NA	9.70E-08	mr1977_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