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Detailed information for vg0127517746:

Variant ID: vg0127517746 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 27517746
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGTTCACTGGTGGAGAAATGCTTTTTAGTCCCGGTTCGTAACCCCCTGTAGTCCCGGTTTTCCAACCGGGACTACGAATCCGGGACTAAAGATCGCTAT[C/T]
TTTAGTCCCGGTTCAAATAACCGGGACTAAAAATCAATCTTTAGTCCCGGTTAATGTTACCAACCGGGACTAAAGATGGGAGAATCTTTAGTCCCGGTTC

Reverse complement sequence

GAACCGGGACTAAAGATTCTCCCATCTTTAGTCCCGGTTGGTAACATTAACCGGGACTAAAGATTGATTTTTAGTCCCGGTTATTTGAACCGGGACTAAA[G/A]
ATAGCGATCTTTAGTCCCGGATTCGTAGTCCCGGTTGGAAAACCGGGACTACAGGGGGTTACGAACCGGGACTAAAAAGCATTTCTCCACCAGTGAACCG

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	48.50%	1.20%	2.16%	48.16%	NA
All Indica	2759	20.20%	0.00%	2.54%	77.24%	NA
All Japonica	1512	93.70%	3.60%	1.92%	0.79%	NA
Aus	269	79.90%	0.00%	0.37%	19.70%	NA
Indica I	595	13.40%	0.00%	2.35%	84.20%	NA
Indica II	465	20.00%	0.00%	1.29%	78.71%	NA
Indica III	913	23.30%	0.00%	3.50%	73.17%	NA
Indica Intermediate	786	21.90%	0.00%	2.29%	75.83%	NA
Temperate Japonica	767	91.00%	5.50%	3.13%	0.39%	NA
Tropical Japonica	504	98.80%	0.00%	0.60%	0.60%	NA
Japonica Intermediate	241	91.30%	5.40%	0.83%	2.49%	NA
VI/Aromatic	96	47.90%	0.00%	1.04%	51.04%	NA
Intermediate	90	63.30%	1.10%	1.11%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0127517746	C -> T	LOC_Os01g48060-LOC_Os01g48070	intergenic_region ; MODIFIER	silent_mutation	Average:18.829; most accessible tissue: Callus, score: 31.544	N	N	N	N
vg0127517746	C -> DEL	N	N	silent_mutation	Average:18.829; most accessible tissue: Callus, score: 31.544	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0127517746	8.48E-09	8.48E-09	mr1024_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
vg0127517746	NA	2.55E-06	mr1167_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
vg0127517746	NA	9.91E-06	mr1565_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
vg0127517746	NA	5.19E-07	mr1726_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
vg0127517746	8.96E-07	8.96E-07	mr1950_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