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Detailed information for vg0722037032:

Variant ID: vg0722037032 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 22037032
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTAACATGTGCAGTCAGGCCTCCTCATAGGTTAAACATAAAAATTCTAATACATGGTGGATGGCTCAATGTGTTAGTTCGTGATAGCTCAATTATGTG[C/T]
TATTAATATACAGAAGGCATGGAACTACAGAACTACAGAAAAGCATAGCATATGTACAACATGAGTCACTCATATTACTCTCAAATACGTAAATGTCTTT

Reverse complement sequence

AAAGACATTTACGTATTTGAGAGTAATATGAGTGACTCATGTTGTACATATGCTATGCTTTTCTGTAGTTCTGTAGTTCCATGCCTTCTGTATATTAATA[G/A]
CACATAATTGAGCTATCACGAACTAACACATTGAGCCATCCACCATGTATTAGAATTTTTATGTTTAACCTATGAGGAGGCCTGACTGCACATGTTAACA

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	89.20%	10.80%	0.00%	0.00%	NA
All Indica	2759	87.40%	12.60%	0.00%	0.00%	NA
All Japonica	1512	94.30%	5.70%	0.00%	0.00%	NA
Aus	269	74.30%	25.70%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	80.60%	19.40%	0.00%	0.00%	NA
Indica III	913	80.90%	19.10%	0.00%	0.00%	NA
Indica Intermediate	786	89.60%	10.40%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	86.30%	13.70%	0.00%	0.00%	NA
Japonica Intermediate	241	93.40%	6.60%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	0.00%	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
vg0722037032	C -> T	LOC_Os07g36780.1	3_prime_UTR_variant ; 128.0bp to feature; MODIFIER	silent_mutation	Average:53.195; most accessible tissue: Callus, score: 83.434	N	N	N	N
vg0722037032	C -> T	LOC_Os07g36770.1	upstream_gene_variant ; 2172.0bp to feature; MODIFIER	silent_mutation	Average:53.195; most accessible tissue: Callus, score: 83.434	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0722037032	NA	7.21E-08	mr1188	Ind_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
vg0722037032	NA	5.59E-08	mr1188_2	Ind_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