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Detailed information for vg1002308179:

Variant ID: vg1002308179 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 2308179
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGCTCACAACCCACCATTATCAAATTTTAGTTGGCACATTAATTAATCAACCAATCACGATTGACCATCGTGAGCTATCATTAAGCCATCATTAAATAA[C/T]
AGTGAAGCATTAGTTATCCCAATTGTGTGCTAATGTTTCTAAGCATGGCTAAGCAATTATGTCTAACATCTAGCTGAACCAATATATAAAGCTCAACTAG

Reverse complement sequence

CTAGTTGAGCTTTATATATTGGTTCAGCTAGATGTTAGACATAATTGCTTAGCCATGCTTAGAAACATTAGCACACAATTGGGATAACTAATGCTTCACT[G/A]
TTATTTAATGATGGCTTAATGATAGCTCACGATGGTCAATCGTGATTGGTTGATTAATTAATGTGCCAACTAAAATTTGATAATGGTGGGTTGTGAGCAC

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	79.30%	19.40%	0.08%	1.18%	NA
All Indica	2759	96.10%	2.70%	0.04%	1.16%	NA
All Japonica	1512	46.60%	51.80%	0.20%	1.39%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.20%	0.00%	0.22%	NA
Indica III	913	92.00%	5.10%	0.11%	2.74%	NA
Indica Intermediate	786	96.60%	2.70%	0.00%	0.76%	NA
Temperate Japonica	767	50.10%	49.90%	0.00%	0.00%	NA
Tropical Japonica	504	27.80%	67.50%	0.60%	4.17%	NA
Japonica Intermediate	241	75.10%	24.90%	0.00%	0.00%	NA
VI/Aromatic	96	59.40%	39.60%	0.00%	1.04%	NA
Intermediate	90	81.10%	16.70%	0.00%	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
vg1002308179	C -> T	LOC_Os10g04780-LOC_Os10g04800	intergenic_region ; MODIFIER	silent_mutation	Average:14.984; most accessible tissue: Minghui63 flag leaf, score: 23.551	N	N	N	N
vg1002308179	C -> DEL	N	N	silent_mutation	Average:14.984; most accessible tissue: Minghui63 flag leaf, score: 23.551	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1002308179	NA	1.68E-07	mr1606	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
vg1002308179	NA	3.36E-09	mr1709_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