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Detailed information for vg0112234029:

Variant ID: vg0112234029 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 12234029
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTGGACTGCAGAAGCATAAGAAACGTCTTCAAAAAGAATATCAGAAACATCAGAATCTTCTTGAACAAAAAGACCAACAGTTACCTATTGTTGACAATA[C/A]
CAATACCAGTTCTATCCAACAAAAAAATATGCATTATGGTAAGTATGATAGCATGAACAATCAACCACTGGTTCTATCAGAATCCTGCTACAATGAACAT

Reverse complement sequence

ATGTTCATTGTAGCAGGATTCTGATAGAACCAGTGGTTGATTGTTCATGCTATCATACTTACCATAATGCATATTTTTTTGTTGGATAGAACTGGTATTG[G/T]
TATTGTCAACAATAGGTAACTGTTGGTCTTTTTGTTCAAGAAGATTCTGATGTTTCTGATATTCTTTTTGAAGACGTTTCTTATGCTTCTGCAGTCCACA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.60%	1.40%	0.95%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	92.70%	4.40%	2.91%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	85.80%	8.60%	5.61%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0112234029	C -> A	LOC_Os01g21810.1	missense_variant ; p.Thr146Asn; MODERATE	nonsynonymous_codon ; T146N	Average:45.873; most accessible tissue: Callus, score: 80.594	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112234029	2.93E-06	2.93E-06	mr1373	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
vg0112234029	NA	1.08E-09	mr1648	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
vg0112234029	NA	1.35E-07	mr1164_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