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Detailed information for vg0119798012:

Variant ID: vg0119798012 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 19798012
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCACAGCCGGCGGTTGAGTCAACTACCTGGTCAATGCGAGGCAACCCAAAAGGATCTTTGGGGCAAGACTTGTTGAGGTCGGTATAATCAACACACATG[A/C]
GCCATTGCCCTGTTTTCTTCCGAACTAGAACCGGGTTTGCCAGCCAGTCGGGATGAAGGACTTCTTTGATGAAGCCTGCTGCTAACAGCTTGGTTAATTC

Reverse complement sequence

GAATTAACCAAGCTGTTAGCAGCAGGCTTCATCAAAGAAGTCCTTCATCCCGACTGGCTGGCAAACCCGGTTCTAGTTCGGAAGAAAACAGGGCAATGGC[T/G]
CATGTGTGTTGATTATACCGACCTCAACAAGTCTTGCCCCAAAGATCCTTTTGGGTTGCCTCGCATTGACCAGGTAGTTGACTCAACCGCCGGCTGTGAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.20%	0.20%	6.81%	21.75%	NA
All Indica	2759	54.20%	0.30%	10.69%	34.76%	NA
All Japonica	1512	98.80%	0.00%	0.60%	0.60%	NA
Aus	269	75.50%	0.00%	5.95%	18.59%	NA
Indica I	595	64.90%	0.70%	9.08%	25.38%	NA
Indica II	465	73.10%	0.20%	7.74%	18.92%	NA
Indica III	913	32.60%	0.10%	14.02%	53.23%	NA
Indica Intermediate	786	60.10%	0.40%	9.80%	29.77%	NA
Temperate Japonica	767	99.10%	0.00%	0.52%	0.39%	NA
Tropical Japonica	504	98.80%	0.00%	0.60%	0.60%	NA
Japonica Intermediate	241	97.90%	0.00%	0.83%	1.24%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	87.80%	0.00%	2.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0119798012	A -> DEL	LOC_Os01g35740.1	N	frameshift_variant	Average:17.719; most accessible tissue: Minghui63 young leaf, score: 39.381	N	N	N	N
vg0119798012	A -> C	LOC_Os01g35740.1	missense_variant ; p.Leu1053Arg; MODERATE	nonsynonymous_codon ; L1053R	Average:17.719; most accessible tissue: Minghui63 young leaf, score: 39.381	possibly damaging	-1.811	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0119798012	1.06E-06	1.06E-06	mr1966	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
vg0119798012	4.40E-06	4.40E-06	mr1966	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