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Detailed information for vg0101822336:

Variant ID: vg0101822336 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 1822336
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.01, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCCCTGAGAAGAGGCTACCACTGCGTCCGTTAGTCGACTGGCAGCCTCGCGTATCTGATCGCTGAAGACAAGGGATCCATCAACTGGGTTAAGCATTC[C/A]
ACCGTGAGCATAGTACCAAAACTTCGATCTATCCGGCCATTTAGCGGTGGCCGGTTCGATACCCCTCTCAATCAAACTTGCCTCCATCTCCTCCCACTTC

Reverse complement sequence

GAAGTGGGAGGAGATGGAGGCAAGTTTGATTGAGAGGGGTATCGAACCGGCCACCGCTAAATGGCCGGATAGATCGAAGTTTTGGTACTATGCTCACGGT[G/T]
GAATGCTTAACCCAGTTGATGGATCCCTTGTCTTCAGCGATCAGATACGCGAGGCTGCCAGTCGACTAACGGACGCAGTGGTAGCCTCTTCTCAGGGCAC

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	75.30%	23.30%	1.35%	0.00%	NA
All Indica	2759	69.70%	29.50%	0.76%	0.00%	NA
All Japonica	1512	81.90%	16.10%	2.05%	0.00%	NA
Aus	269	89.60%	6.70%	3.72%	0.00%	NA
Indica I	595	38.00%	61.50%	0.50%	0.00%	NA
Indica II	465	75.70%	23.70%	0.65%	0.00%	NA
Indica III	913	83.50%	16.00%	0.55%	0.00%	NA
Indica Intermediate	786	74.30%	24.40%	1.27%	0.00%	NA
Temperate Japonica	767	97.70%	2.00%	0.39%	0.00%	NA
Tropical Japonica	504	58.50%	40.90%	0.60%	0.00%	NA
Japonica Intermediate	241	80.50%	9.10%	10.37%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	68.90%	30.00%	1.11%	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
vg0101822336	C -> A	LOC_Os01g04140.1	stop_gained ; p.Gly61*; HIGH	stop_gained	Average:17.382; most accessible tissue: Zhenshan97 root, score: 27.411	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0101822336	NA	2.64E-06	mr1213	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
vg0101822336	NA	4.57E-08	mr1224	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
vg0101822336	NA	3.82E-07	mr1225	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
vg0101822336	NA	2.09E-07	mr1746	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
vg0101822336	NA	6.10E-06	mr1158_2	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
vg0101822336	NA	5.65E-13	mr1769_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