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Detailed information for vg0719707311:

Variant ID: vg0719707311 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 19707311
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGCCTAGTCTCTTCAAAATACTCAAAGGGGTATTTGCATGTGTGCGTTCACAGAAGTGATTGTGCACGCGTTGTGAGCGCCCGCGTTTGTACTTTGTTT[A/C]
AAAAAAACATCAAACATTATTTATTGTTTCTCTTTTATTTAATAGATAAAACAATAGGGAGGGGATGGCAGTGTTGTGTACATGTGATGGTGAGGAGGTG

Reverse complement sequence

CACCTCCTCACCATCACATGTACACAACACTGCCATCCCCTCCCTATTGTTTTATCTATTAAATAAAAGAGAAACAATAAATAATGTTTGATGTTTTTTT[T/G]
AAACAAAGTACAAACGCGGGCGCTCACAACGCGTGCACAATCACTTCTGTGAACGCACACATGCAAATACCCCTTTGAGTATTTTGAAGAGACTAGGCTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.80%	1.70%	2.31%	5.21%	NA
All Indica	2759	96.40%	0.20%	3.12%	0.25%	NA
All Japonica	1512	78.30%	5.00%	1.06%	15.67%	NA
Aus	269	98.10%	0.00%	1.86%	0.00%	NA
Indica I	595	98.30%	0.00%	1.68%	0.00%	NA
Indica II	465	95.70%	0.00%	3.66%	0.65%	NA
Indica III	913	95.20%	0.00%	4.71%	0.11%	NA
Indica Intermediate	786	96.80%	0.80%	2.04%	0.38%	NA
Temperate Japonica	767	58.50%	9.60%	1.43%	30.38%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	96.30%	0.00%	2.07%	1.66%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	0.00%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0719707311	A -> DEL	N	N	silent_mutation	Average:23.169; most accessible tissue: Minghui63 root, score: 40.262	N	N	N	N
vg0719707311	A -> C	LOC_Os07g32990.1	upstream_gene_variant ; 2173.0bp to feature; MODIFIER	silent_mutation	Average:23.169; most accessible tissue: Minghui63 root, score: 40.262	N	N	N	N
vg0719707311	A -> C	LOC_Os07g32979.1	downstream_gene_variant ; 3290.0bp to feature; MODIFIER	silent_mutation	Average:23.169; most accessible tissue: Minghui63 root, score: 40.262	N	N	N	N
vg0719707311	A -> C	LOC_Os07g32979-LOC_Os07g32990	intergenic_region ; MODIFIER	silent_mutation	Average:23.169; most accessible tissue: Minghui63 root, score: 40.262	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0719707311	4.30E-06	4.30E-06	mr1861	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