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Detailed information for vg1014017091:

Variant ID: vg1014017091 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 14017091
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTGGCAGTGGAGCCCAGTGGTGGGCAGATCCACCACCTCCGCTGTTACAGTGACGGCATCTTCTGAGGCGGTGGGAATGGGAGCTTCTGGCTAGGGATC[C/T,A]
TGGATTTTTTTTTTTGAATTTTCAAATTTTTTGGTGATTTTCTGGTGACATAATGCACCGCATGCAAAAGTTCATTATGGCACGTGATTCAGCCGCTCGG

Reverse complement sequence

CCGAGCGGCTGAATCACGTGCCATAATGAACTTTTGCATGCGGTGCATTATGTCACCAGAAAATCACCAAAAAATTTGAAAATTCAAAAAAAAAAATCCA[G/A,T]
GATCCCTAGCCAGAAGCTCCCATTCCCACCGCCTCAGAAGATGCCGTCACTGTAACAGCGGAGGTGGTGGATCTGCCCACCACTGGGCTCCACTGCCACC

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	93.20%	6.50%	0.11%	0.00%	A: 0.15%
All Indica	2759	99.50%	0.50%	0.00%	0.00%	NA
All Japonica	1512	81.00%	18.80%	0.26%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.90%	0.00%	0.00%	NA
Temperate Japonica	767	95.80%	4.20%	0.00%	0.00%	NA
Tropical Japonica	504	54.00%	45.20%	0.79%	0.00%	NA
Japonica Intermediate	241	90.00%	10.00%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	1.00%	0.00%	0.00%	A: 4.17%
Intermediate	90	83.30%	12.20%	1.11%	0.00%	A: 3.33%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1014017091	C -> T	LOC_Os10g26780.1	upstream_gene_variant ; 3258.0bp to feature; MODIFIER	silent_mutation	Average:53.549; most accessible tissue: Zhenshan97 young leaf, score: 75.751	N	N	N	N
vg1014017091	C -> T	LOC_Os10g26780-LOC_Os10g26800	intergenic_region ; MODIFIER	silent_mutation	Average:53.549; most accessible tissue: Zhenshan97 young leaf, score: 75.751	N	N	N	N
vg1014017091	C -> A	LOC_Os10g26780.1	upstream_gene_variant ; 3258.0bp to feature; MODIFIER	silent_mutation	Average:53.549; most accessible tissue: Zhenshan97 young leaf, score: 75.751	N	N	N	N
vg1014017091	C -> A	LOC_Os10g26780-LOC_Os10g26800	intergenic_region ; MODIFIER	silent_mutation	Average:53.549; most accessible tissue: Zhenshan97 young leaf, score: 75.751	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1014017091	NA	8.75E-06	mr1125	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
vg1014017091	NA	6.05E-06	mr1039_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
vg1014017091	2.60E-06	2.60E-06	mr1325_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
vg1014017091	NA	2.88E-09	mr1379_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
vg1014017091	NA	3.20E-07	mr1401_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
vg1014017091	NA	1.64E-07	mr1623_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
vg1014017091	NA	2.00E-08	mr1819_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
vg1014017091	NA	1.34E-10	mr1905_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