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Detailed information for vg0707032320:

Variant ID: vg0707032320 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 7032320
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

TATCATACCAGGATATATCACGTCCTGTATGAGATTGGCTTATTTTGGGACAGAGAGAGTATCTTTTTTGGTGAATGATACAGTAGGTTTAGGAGGCATC[C/T]
GGACTAGTACATAGCTTAAACTCAATGTGGTTGACAGTGAAGTGGAGAAATCAAGGGAGATATATAGGGCCTGTTTGGTACAGCTCTAACTCCTAAATTT

Reverse complement sequence

AAATTTAGGAGTTAGAGCTGTACCAAACAGGCCCTATATATCTCCCTTGATTTCTCCACTTCACTGTCAACCACATTGAGTTTAAGCTATGTACTAGTCC[G/A]
GATGCCTCCTAAACCTACTGTATCATTCACCAAAAAAGATACTCTCTCTGTCCCAAAATAAGCCAATCTCATACAGGACGTGATATATCCTGGTATGATA

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	95.80%	3.60%	0.61%	0.00%	NA
All Indica	2759	99.70%	0.20%	0.11%	0.00%	NA
All Japonica	1512	93.70%	4.90%	1.39%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.40%	0.38%	0.00%	NA
Temperate Japonica	767	92.60%	5.10%	2.35%	0.00%	NA
Tropical Japonica	504	97.60%	2.40%	0.00%	0.00%	NA
Japonica Intermediate	241	89.20%	9.50%	1.24%	0.00%	NA
VI/Aromatic	96	14.60%	83.30%	2.08%	0.00%	NA
Intermediate	90	88.90%	8.90%	2.22%	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
vg0707032320	C -> T	LOC_Os07g12370.1	downstream_gene_variant ; 305.0bp to feature; MODIFIER	silent_mutation	Average:64.519; most accessible tissue: Callus, score: 85.102	N	N	N	N
vg0707032320	C -> T	LOC_Os07g12360-LOC_Os07g12370	intergenic_region ; MODIFIER	silent_mutation	Average:64.519; most accessible tissue: Callus, score: 85.102	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0707032320	3.97E-08	NA	mr1757	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
vg0707032320	NA	1.58E-08	mr1757	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
vg0707032320	NA	1.60E-07	mr1829	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
vg0707032320	6.35E-06	NA	mr1310_2	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
vg0707032320	NA	3.16E-06	mr1549_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
vg0707032320	NA	8.68E-07	mr1567_2	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
vg0707032320	5.01E-06	NA	mr1757_2	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
vg0707032320	NA	3.65E-07	mr1757_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
vg0707032320	NA	1.48E-10	mr1829_2	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