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Detailed information for vg0131782604:

Variant ID: vg0131782604 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 31782604
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAATTCCAAGGAAACGGTCCTTAAGTGCAAGAGCGGGAAACTGTACACCCGGTACGTTCCCCGGTCCTCAGTTTTGGAAATTCATTTAGTTCGCAAGCA[C/T]
CGACCCAAGTGTCGGGTTTTCCAAGTCTTTTGTAAAACCCAAGTTTTACCCAAGATGTTTCTCAGATTTTAAGTTTGAAGGCGACCGTTGATACCCGTGC

Reverse complement sequence

GCACGGGTATCAACGGTCGCCTTCAAACTTAAAATCTGAGAAACATCTTGGGTAAAACTTGGGTTTTACAAAAGACTTGGAAAACCCGACACTTGGGTCG[G/A]
TGCTTGCGAACTAAATGAATTTCCAAAACTGAGGACCGGGGAACGTACCGGGTGTACAGTTTCCCGCTCTTGCACTTAAGGACCGTTTCCTTGGAATTTC

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	81.60%	1.60%	11.07%	5.71%	NA
All Indica	2759	76.30%	2.80%	16.31%	4.68%	NA
All Japonica	1512	91.10%	0.00%	3.44%	5.42%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.80%	0.20%	2.52%	1.51%	NA
Indica II	465	95.90%	0.60%	3.23%	0.22%	NA
Indica III	913	52.10%	5.40%	33.73%	8.76%	NA
Indica Intermediate	786	77.90%	2.90%	14.25%	4.96%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	75.60%	0.00%	9.13%	15.28%	NA
Japonica Intermediate	241	96.30%	0.00%	2.49%	1.24%	NA
VI/Aromatic	96	32.30%	0.00%	16.67%	51.04%	NA
Intermediate	90	83.30%	0.00%	5.56%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0131782604	C -> T	LOC_Os01g55220-LOC_Os01g55240	intergenic_region ; MODIFIER	silent_mutation	Average:22.713; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N
vg0131782604	C -> DEL	N	N	silent_mutation	Average:22.713; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0131782604	1.95E-07	NA	mr1275	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
vg0131782604	8.92E-07	8.92E-07	mr1275	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
vg0131782604	NA	4.34E-06	mr1286	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
vg0131782604	7.49E-06	1.79E-06	mr1392	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
vg0131782604	NA	2.63E-07	mr1723_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