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Detailed information for vg0100783830:

Variant ID: vg0100783830 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 783830
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGTATACAAAGGACGACTACCAAACGGAGTGCCTGTGGCAGTTAAAATGATAGAACACTCTACAGGAAATGGAGAAGAGTTCATCAATGAAGTAGCAAC[A/C]
ATTGGACAAATTCATCATATAAACATTGCCCGCCTTCTGGGATTCTGCTCTGAAGGAACACGGCACATTCTTATCTATGAATTCATGCCTAATGAATCAT

Reverse complement sequence

ATGATTCATTAGGCATGAATTCATAGATAAGAATGTGCCGTGTTCCTTCAGAGCAGAATCCCAGAAGGCGGGCAATGTTTATATGATGAATTTGTCCAAT[T/G]
GTTGCTACTTCATTGATGAACTCTTCTCCATTTCCTGTAGAGTGTTCTATCATTTTAACTGCCACAGGCACTCCGTTTGGTAGTCGTCCTTTGTATACAC

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	87.20%	1.10%	3.03%	8.68%	NA
All Indica	2759	98.20%	0.50%	0.76%	0.62%	NA
All Japonica	1512	77.20%	0.10%	0.93%	21.76%	NA
Aus	269	55.00%	11.50%	30.86%	2.60%	NA
Indica I	595	99.70%	0.20%	0.00%	0.17%	NA
Indica II	465	98.30%	0.00%	0.43%	1.29%	NA
Indica III	913	98.80%	0.50%	0.33%	0.33%	NA
Indica Intermediate	786	96.20%	0.90%	2.04%	0.89%	NA
Temperate Japonica	767	77.40%	0.00%	0.78%	21.77%	NA
Tropical Japonica	504	83.70%	0.00%	0.99%	15.28%	NA
Japonica Intermediate	241	63.10%	0.40%	1.24%	35.27%	NA
VI/Aromatic	96	22.90%	4.20%	21.88%	51.04%	NA
Intermediate	90	83.30%	3.30%	4.44%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0100783830	A -> DEL	LOC_Os01g02420.1	N	frameshift_variant	Average:47.359; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg0100783830	A -> C	LOC_Os01g02420.1	synonymous_variant ; p.Thr383Thr; LOW	synonymous_codon	Average:47.359; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0100783830	3.66E-06	6.44E-07	mr1725	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