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Detailed information for vg0134200751:

Variant ID: vg0134200751 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 34200751
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGGAGTATCTGATTCTACCAGGCAACAGCCGCAACAGGACAAGACCCTATCAAGCAGGGGAGCTAGCTCCTATGGTGGGATGGACCTACTGCAACCCTG[T/C]
TTAGATGGGACTAAAACTTTCAAGTCCCTATCACATCAGATGTTTGGACACTAATATAAATATTAAACGTAGACTATTAATAAAACCCATCCATAATCTT

Reverse complement sequence

AAGATTATGGATGGGTTTTATTAATAGTCTACGTTTAATATTTATATTAGTGTCCAAACATCTGATGTGATAGGGACTTGAAAGTTTTAGTCCCATCTAA[A/G]
CAGGGTTGCAGTAGGTCCATCCCACCATAGGAGCTAGCTCCCCTGCTTGATAGGGTCTTGTCCTGTTGCGGCTGTTGCCTGGTAGAATCAGATACTCCCT

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	94.90%	4.40%	0.66%	0.00%	NA
All Indica	2759	99.80%	0.10%	0.07%	0.00%	NA
All Japonica	1512	89.90%	8.60%	1.52%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.30%	0.13%	0.00%	NA
Temperate Japonica	767	98.30%	0.80%	0.91%	0.00%	NA
Tropical Japonica	504	75.60%	22.00%	2.38%	0.00%	NA
Japonica Intermediate	241	92.90%	5.40%	1.66%	0.00%	NA
VI/Aromatic	96	31.20%	66.70%	2.08%	0.00%	NA
Intermediate	90	81.10%	14.40%	4.44%	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
vg0134200751	T -> C	LOC_Os01g59200.1	upstream_gene_variant ; 768.0bp to feature; MODIFIER	silent_mutation	Average:48.883; most accessible tissue: Zhenshan97 flower, score: 75.883	N	N	N	N
vg0134200751	T -> C	LOC_Os01g59210.1	upstream_gene_variant ; 4485.0bp to feature; MODIFIER	silent_mutation	Average:48.883; most accessible tissue: Zhenshan97 flower, score: 75.883	N	N	N	N
vg0134200751	T -> C	LOC_Os01g59190-LOC_Os01g59200	intergenic_region ; MODIFIER	silent_mutation	Average:48.883; most accessible tissue: Zhenshan97 flower, score: 75.883	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0134200751	4.21E-06	4.21E-06	mr1850	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