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Detailed information for vg0719016083:

Variant ID: vg0719016083 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 19016083
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAAACTGACTGGTTGCATGGCGGCGCTCAGCCGGTTCATTTCACGACTCGGCGAGTGGGGGATGCCCTTCTTCAAGCTGCTGAAGAAGACTGACAATTT[T/C]
CAGTGGGGACCCGAAGCAAAAAAAGCCTTTGAAGACTTCAAGAAACTTCTCACCACTCCACCAGTTTTGGCCTCACCACGTCCACAAGAGCCGCTACTGT

Reverse complement sequence

ACAGTAGCGGCTCTTGTGGACGTGGTGAGGCCAAAACTGGTGGAGTGGTGAGAAGTTTCTTGAAGTCTTCAAAGGCTTTTTTTGCTTCGGGTCCCCACTG[A/G]
AAATTGTCAGTCTTCTTCAGCAGCTTGAAGAAGGGCATCCCCCACTCGCCGAGTCGTGAAATGAACCGGCTGAGCGCCGCCATGCAACCAGTCAGTTTTT

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	46.00%	0.30%	9.71%	44.05%	NA
All Indica	2759	31.20%	0.40%	8.34%	60.09%	NA
All Japonica	1512	73.00%	0.00%	10.98%	16.01%	NA
Aus	269	49.40%	0.40%	12.27%	37.92%	NA
Indica I	595	15.30%	0.20%	7.06%	77.48%	NA
Indica II	465	28.00%	0.40%	7.74%	63.87%	NA
Indica III	913	41.20%	0.40%	10.95%	47.43%	NA
Indica Intermediate	786	33.50%	0.50%	6.62%	59.41%	NA
Temperate Japonica	767	96.70%	0.00%	0.65%	2.61%	NA
Tropical Japonica	504	43.10%	0.00%	25.00%	31.94%	NA
Japonica Intermediate	241	60.20%	0.00%	14.52%	25.31%	NA
VI/Aromatic	96	35.40%	0.00%	16.67%	47.92%	NA
Intermediate	90	46.70%	0.00%	15.56%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0719016083	T -> DEL	N	N	silent_mutation	Average:6.24; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N
vg0719016083	T -> C	LOC_Os07g31980.1	downstream_gene_variant ; 2568.0bp to feature; MODIFIER	silent_mutation	Average:6.24; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N
vg0719016083	T -> C	LOC_Os07g31960-LOC_Os07g31980	intergenic_region ; MODIFIER	silent_mutation	Average:6.24; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0719016083	NA	8.54E-06	mr1131	Ind_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
vg0719016083	NA	1.60E-08	mr1213	Ind_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
vg0719016083	3.57E-06	NA	mr1088_2	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
vg0719016083	5.82E-06	6.97E-07	mr1088_2	Ind_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
vg0719016083	NA	8.84E-06	mr1131_2	Ind_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
vg0719016083	NA	7.01E-09	mr1212_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
vg0719016083	NA	1.20E-06	mr1212_2	Ind_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
vg0719016083	NA	2.56E-06	mr1233_2	Ind_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
vg0719016083	9.23E-07	NA	mr1246_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
vg0719016083	NA	3.10E-06	mr1246_2	Ind_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
vg0719016083	1.62E-06	NA	mr1404_2	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
vg0719016083	2.37E-06	3.09E-08	mr1404_2	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
vg0719016083	NA	7.62E-06	mr1439_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
vg0719016083	NA	7.14E-07	mr1439_2	Ind_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
vg0719016083	7.64E-07	NA	mr1620_2	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
vg0719016083	9.71E-07	5.20E-08	mr1620_2	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