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Detailed information for vg1003385190:

Variant ID: vg1003385190 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3385190
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGGTATTTCTTACGACCACGGATAAATCCGCAAGCGCACGGAATACCGCTGTAGCACTTCACCTTCGGGTGACCCATAAAGGATATCGAACTCAGGGAA[C/T]
GTGTGTAATCTACCTAAGGCTAAGACTATCCAAGGACAACAACTGATGGTAGGCAGGCTAGAGAGGACTTTCTATGAGTGTTAATTATCTACGCTAAGCA

Reverse complement sequence

TGCTTAGCGTAGATAATTAACACTCATAGAAAGTCCTCTCTAGCCTGCCTACCATCAGTTGTTGTCCTTGGATAGTCTTAGCCTTAGGTAGATTACACAC[G/A]
TTCCCTGAGTTCGATATCCTTTATGGGTCACCCGAAGGTGAAGTGCTACAGCGGTATTCCGTGCGCTTGCGGATTTATCCGTGGTCGTAAGAAATACCAA

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	86.90%	0.50%	5.31%	7.30%	NA
All Indica	2759	87.20%	0.00%	2.10%	10.69%	NA
All Japonica	1512	84.30%	1.20%	11.77%	2.78%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	70.90%	0.00%	4.54%	24.54%	NA
Indica II	465	93.80%	0.00%	1.72%	4.52%	NA
Indica III	913	92.80%	0.00%	0.55%	6.68%	NA
Indica Intermediate	786	89.10%	0.10%	2.29%	8.52%	NA
Temperate Japonica	767	76.70%	2.20%	18.12%	3.00%	NA
Tropical Japonica	504	96.40%	0.00%	2.78%	0.79%	NA
Japonica Intermediate	241	83.00%	0.40%	10.37%	6.22%	NA
VI/Aromatic	96	83.30%	4.20%	11.46%	1.04%	NA
Intermediate	90	88.90%	0.00%	4.44%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003385190	C -> T	LOC_Os10g06560-LOC_Os10g06580	intergenic_region ; MODIFIER	silent_mutation	Average:33.235; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg1003385190	C -> DEL	N	N	silent_mutation	Average:33.235; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003385190	NA	7.29E-06	mr1395	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
vg1003385190	2.15E-07	2.15E-07	mr1542	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
vg1003385190	NA	1.63E-07	mr1613	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