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Detailed information for vg0717573276:

Variant ID: vg0717573276 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 17573276
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTAATAATTATTTAAATTTTTTGAATAAGACGAGCGGTCAAACATGTGCTAAAAAGTCAACGGTGTCAAATAAAACGAAACGGAGGGAGTACTATTTT[T/C]
CTGAGTATCATATACTACCTATTGTTTTTTCGGGTGCATTATTCACTCCTCGATCATTTACGCGCCTACGTGGTCGATTTTTCTGAATCCGTCCGATCGT

Reverse complement sequence

ACGATCGGACGGATTCAGAAAAATCGACCACGTAGGCGCGTAAATGATCGAGGAGTGAATAATGCACCCGAAAAAACAATAGGTAGTATATGATACTCAG[A/G]
AAAATAGTACTCCCTCCGTTTCGTTTTATTTGACACCGTTGACTTTTTAGCACATGTTTGACCGCTCGTCTTATTCAAAAAATTTAAATAATTATTAATT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.30%	5.10%	1.82%	37.81%	NA
All Indica	2759	43.00%	0.10%	1.27%	55.64%	NA
All Japonica	1512	71.90%	15.10%	2.84%	10.19%	NA
Aus	269	73.20%	0.00%	0.74%	26.02%	NA
Indica I	595	51.80%	0.00%	1.85%	46.39%	NA
Indica II	465	20.90%	0.20%	2.37%	76.56%	NA
Indica III	913	43.00%	0.20%	0.33%	56.41%	NA
Indica Intermediate	786	49.20%	0.10%	1.27%	49.36%	NA
Temperate Japonica	767	93.90%	3.50%	1.96%	0.65%	NA
Tropical Japonica	504	44.00%	29.80%	3.77%	22.42%	NA
Japonica Intermediate	241	60.20%	21.20%	3.73%	14.94%	NA
VI/Aromatic	96	93.80%	0.00%	1.04%	5.21%	NA
Intermediate	90	58.90%	10.00%	5.56%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0717573276	T -> DEL	N	N	silent_mutation	Average:19.099; most accessible tissue: Callus, score: 92.503	N	N	N	N
vg0717573276	T -> C	LOC_Os07g29860.1	downstream_gene_variant ; 751.0bp to feature; MODIFIER	silent_mutation	Average:19.099; most accessible tissue: Callus, score: 92.503	N	N	N	N
vg0717573276	T -> C	LOC_Os07g29860-LOC_Os07g29870	intergenic_region ; MODIFIER	silent_mutation	Average:19.099; most accessible tissue: Callus, score: 92.503	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0717573276	8.42E-06	NA	mr1200_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
vg0717573276	4.50E-06	6.46E-14	mr1993_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