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Detailed information for vg0710326243:

Variant ID: vg0710326243 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10326243
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCATCTAGAAGCCATAATCATGAAATAAACTCAGATATCCAAACAAACAACCCGAAACCAAAACCGATACAGTGTCGGCCGGTCAGATCGCGGGCTGCGT[C/T]
GGTCTGACCGCGCATTACACGCCGGTCTGACCGGCTACCAGAGCCCGGTCTGACCGGTCACATGAAATAATGAATCCTGCGATCACCTGTGAATCCAATC

Reverse complement sequence

GATTGGATTCACAGGTGATCGCAGGATTCATTATTTCATGTGACCGGTCAGACCGGGCTCTGGTAGCCGGTCAGACCGGCGTGTAATGCGCGGTCAGACC[G/A]
ACGCAGCCCGCGATCTGACCGGCCGACACTGTATCGGTTTTGGTTTCGGGTTGTTTGTTTGGATATCTGAGTTTATTTCATGATTATGGCTTCTAGATGG

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	59.70%	38.40%	0.36%	1.54%	NA
All Indica	2759	95.30%	4.70%	0.07%	0.00%	NA
All Japonica	1512	1.40%	94.60%	0.00%	4.03%	NA
Aus	269	41.60%	58.40%	0.00%	0.00%	NA
Indica I	595	98.00%	1.80%	0.17%	0.00%	NA
Indica II	465	95.90%	3.90%	0.22%	0.00%	NA
Indica III	913	98.10%	1.90%	0.00%	0.00%	NA
Indica Intermediate	786	89.40%	10.60%	0.00%	0.00%	NA
Temperate Japonica	767	1.70%	98.30%	0.00%	0.00%	NA
Tropical Japonica	504	1.00%	87.30%	0.00%	11.71%	NA
Japonica Intermediate	241	1.20%	97.90%	0.00%	0.83%	NA
VI/Aromatic	96	16.70%	60.40%	15.62%	7.29%	NA
Intermediate	90	48.90%	45.60%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0710326243	C -> DEL	N	N	silent_mutation	Average:36.616; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0710326243	C -> T	LOC_Os07g17480.1	upstream_gene_variant ; 2152.0bp to feature; MODIFIER	silent_mutation	Average:36.616; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0710326243	C -> T	LOC_Os07g17490.1	downstream_gene_variant ; 614.0bp to feature; MODIFIER	silent_mutation	Average:36.616; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0710326243	C -> T	LOC_Os07g17480-LOC_Os07g17490	intergenic_region ; MODIFIER	silent_mutation	Average:36.616; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710326243	1.56E-06	1.56E-06	mr1957	Ind_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