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Detailed information for vg0417772638:

Variant ID: vg0417772638 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17772638
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCAAGTCTAAAAATGCTTATATTCTGGGATGGAGAGAGTAGATATGTAATCCTGATCTCCTGTACACGTATGCTGCAGAATCTCCTATATGTATAGAAA[G/C]
CTCTCTCCTAATCTCTCCTAAAAATATCTCTTGTATTTATAGAAACCTCTCTGTCCTAATATCCATATATGTACGCCATAAAATACATACTGTTCACCAA

Reverse complement sequence

TTGGTGAACAGTATGTATTTTATGGCGTACATATATGGATATTAGGACAGAGAGGTTTCTATAAATACAAGAGATATTTTTAGGAGAGATTAGGAGAGAG[C/G]
TTTCTATACATATAGGAGATTCTGCAGCATACGTGTACAGGAGATCAGGATTACATATCTACTCTCTCCATCCCAGAATATAAGCATTTTTAGACTTGGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.50%	0.10%	3.43%	64.03%	NA
All Indica	2759	37.90%	0.10%	1.63%	60.31%	NA
All Japonica	1512	15.10%	0.10%	3.97%	80.82%	NA
Aus	269	63.20%	0.00%	18.59%	18.22%	NA
Indica I	595	68.90%	0.00%	0.34%	30.76%	NA
Indica II	465	18.10%	0.20%	1.08%	80.65%	NA
Indica III	913	25.80%	0.20%	2.30%	71.63%	NA
Indica Intermediate	786	40.30%	0.00%	2.16%	57.51%	NA
Temperate Japonica	767	11.70%	0.00%	0.26%	88.01%	NA
Tropical Japonica	504	22.40%	0.20%	9.33%	68.06%	NA
Japonica Intermediate	241	10.80%	0.00%	4.56%	84.65%	NA
VI/Aromatic	96	59.40%	0.00%	4.17%	36.46%	NA
Intermediate	90	34.40%	0.00%	3.33%	62.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0417772638	G -> C	LOC_Os04g29820.1	downstream_gene_variant ; 1855.0bp to feature; MODIFIER	silent_mutation	Average:10.596; most accessible tissue: Minghui63 root, score: 19.68	N	N	N	N
vg0417772638	G -> C	LOC_Os04g29810-LOC_Os04g29820	intergenic_region ; MODIFIER	silent_mutation	Average:10.596; most accessible tissue: Minghui63 root, score: 19.68	N	N	N	N
vg0417772638	G -> DEL	N	N	silent_mutation	Average:10.596; most accessible tissue: Minghui63 root, score: 19.68	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417772638	NA	7.96E-06	mr1851	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
vg0417772638	NA	1.30E-10	mr1195_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
vg0417772638	NA	3.98E-06	mr1296_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
vg0417772638	NA	7.93E-09	mr1749_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