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Detailed information for vg0710331329:

Variant ID: vg0710331329 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10331329
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATTCATGTGGAAATGTGGGATGGTTACCTGCAAAGTTGCTCGATGAACCTTCAATTTTATATTACTTTTTATTGATGGTGAATGGTCACGCAAACCTC[T/C]
AATATTTTCTTCTCGGTGGCCTTAATTATGTGTGTAATTGTATGGCTGCACATGGGTGGGAAGAGAAGCTAATTAAGTCACTCTTCGGCTCTTGCATGGG

Reverse complement sequence

CCCATGCAAGAGCCGAAGAGTGACTTAATTAGCTTCTCTTCCCACCCATGTGCAGCCATACAATTACACACATAATTAAGGCCACCGAGAAGAAAATATT[A/G]
GAGGTTTGCGTGACCATTCACCATCAATAAAAAGTAATATAAAATTGAAGGTTCATCGAGCAACTTTGCAGGTAACCATCCCACATTTCCACATGAATAT

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	36.30%	5.70%	0.63%	57.38%	NA
All Indica	2759	8.00%	0.80%	1.01%	90.14%	NA
All Japonica	1512	86.60%	9.10%	0.00%	4.37%	NA
Aus	269	51.30%	9.30%	0.37%	39.03%	NA
Indica I	595	10.60%	0.00%	1.18%	88.24%	NA
Indica II	465	7.30%	0.00%	1.51%	91.18%	NA
Indica III	913	1.50%	1.60%	0.55%	96.28%	NA
Indica Intermediate	786	14.10%	0.90%	1.15%	83.84%	NA
Temperate Japonica	767	81.20%	17.10%	0.00%	1.69%	NA
Tropical Japonica	504	89.90%	0.40%	0.00%	9.72%	NA
Japonica Intermediate	241	96.70%	1.70%	0.00%	1.66%	NA
VI/Aromatic	96	6.20%	78.10%	0.00%	15.62%	NA
Intermediate	90	44.40%	11.10%	1.11%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0710331329	T -> DEL	N	N	silent_mutation	Average:11.778; most accessible tissue: Callus, score: 68.267	N	N	N	N
vg0710331329	T -> C	LOC_Os07g17490.1	upstream_gene_variant ; 2155.0bp to feature; MODIFIER	silent_mutation	Average:11.778; most accessible tissue: Callus, score: 68.267	N	N	N	N
vg0710331329	T -> C	LOC_Os07g17490-LOC_Os07g17500	intergenic_region ; MODIFIER	silent_mutation	Average:11.778; most accessible tissue: Callus, score: 68.267	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710331329	4.80E-06	NA	mr1281	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