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Detailed information for vg0803234769:

Variant ID: vg0803234769 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 3234769
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTAGCAAGAATTTCAACCAGCTGCCTCTTCCATGAGAAAAGGCAACCTGATGATGCAAGTTCGATAGACTACAGATCGATTCCAATCCAACCTCGCCGG[C/T]
GATGGTTCCGAGAAACAGCAGTTGCTGGGCGATGGGACCAACAGCAGACACCGAGGCGGTGCGGAGTCCTCGCCCTCGACCTCGCCGGCGGACGGCGGTA

Reverse complement sequence

TACCGCCGTCCGCCGGCGAGGTCGAGGGCGAGGACTCCGCACCGCCTCGGTGTCTGCTGTTGGTCCCATCGCCCAGCAACTGCTGTTTCTCGGAACCATC[G/A]
CCGGCGAGGTTGGATTGGAATCGATCTGTAGTCTATCGAACTTGCATCATCAGGTTGCCTTTTCTCATGGAAGAGGCAGCTGGTTGAAATTCTTGCTAAG

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	97.80%	1.10%	0.32%	0.76%	NA
All Indica	2759	98.00%	1.70%	0.18%	0.14%	NA
All Japonica	1512	96.70%	0.50%	0.66%	2.12%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.00%	0.00%	0.34%	NA
Indica II	465	98.10%	1.10%	0.86%	0.00%	NA
Indica III	913	95.80%	4.10%	0.11%	0.00%	NA
Indica Intermediate	786	99.20%	0.50%	0.00%	0.25%	NA
Temperate Japonica	767	93.70%	0.80%	1.30%	4.17%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0803234769	C -> T	LOC_Os08g05950.1	downstream_gene_variant ; 4859.0bp to feature; MODIFIER	silent_mutation	Average:63.867; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N
vg0803234769	C -> T	LOC_Os08g05940-LOC_Os08g05950	intergenic_region ; MODIFIER	silent_mutation	Average:63.867; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N
vg0803234769	C -> DEL	N	N	silent_mutation	Average:63.867; most accessible tissue: Minghui63 panicle, score: 82.797	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0803234769	2.73E-06	2.73E-06	mr1927_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