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Detailed information for vg0704371633:

Variant ID: vg0704371633 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 4371633
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACACATGCTTCAAGTGGCTAGGAGGACATCCTCCCTTTTAAGGAGGTCCCCCTCTCCTAGAATAAGCAAGGTGGTACTAAACTCCACATGCATGCCATCC[C/T]
ATGAGGTGGGCTTTTGTGATTTTCCAAAGAATTAATCTTCGAGTGGGCTAAGGCCCATTCATTAATTCCAACATTTAGCCCATGAACTTTTGCATATTAC

Reverse complement sequence

GTAATATGCAAAAGTTCATGGGCTAAATGTTGGAATTAATGAATGGGCCTTAGCCCACTCGAAGATTAATTCTTTGGAAAATCACAAAAGCCCACCTCAT[G/A]
GGATGGCATGCATGTGGAGTTTAGTACCACCTTGCTTATTCTAGGAGAGGGGGACCTCCTTAAAAGGGAGGATGTCCTCCTAGCCACTTGAAGCATGTGT

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	57.50%	1.80%	8.23%	32.48%	NA
All Indica	2759	32.70%	0.00%	13.12%	54.11%	NA
All Japonica	1512	93.20%	5.50%	0.93%	0.40%	NA
Aus	269	89.60%	0.00%	2.97%	7.43%	NA
Indica I	595	24.90%	0.00%	12.10%	63.03%	NA
Indica II	465	42.60%	0.00%	14.19%	43.23%	NA
Indica III	913	29.40%	0.00%	11.94%	58.71%	NA
Indica Intermediate	786	36.80%	0.10%	14.63%	48.47%	NA
Temperate Japonica	767	98.60%	0.30%	0.91%	0.26%	NA
Tropical Japonica	504	92.90%	6.30%	0.40%	0.40%	NA
Japonica Intermediate	241	76.80%	20.30%	2.07%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	1.10%	5.56%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0704371633	C -> DEL	N	N	silent_mutation	Average:20.491; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg0704371633	C -> T	LOC_Os07g08480.1	downstream_gene_variant ; 2583.0bp to feature; MODIFIER	silent_mutation	Average:20.491; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg0704371633	C -> T	LOC_Os07g08480-LOC_Os07g08490	intergenic_region ; MODIFIER	silent_mutation	Average:20.491; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0704371633	2.15E-07	7.59E-11	mr1350_2	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