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Detailed information for vg0136579687:

Variant ID: vg0136579687 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 36579687
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTGCTGGTGCCATTGGTGGGCGTGGAGCTGCACCACGGTTGGGCTGGCCTCCCTGGTGGTTCGGACTGCCGCTAGCGCCCTGGTGGAAGTTGCTAGAGT[G/T]
GAACGGGCGGTGCTGACGGACGATCATGGTGGTAGGTCCACCCTGCTGTCCGGGAGTGAAACGCGGTCGGTGCTGACTACCTTGGTTGGACCGGAACTGC

Reverse complement sequence

GCAGTTCCGGTCCAACCAAGGTAGTCAGCACCGACCGCGTTTCACTCCCGGACAGCAGGGTGGACCTACCACCATGATCGTCCGTCAGCACCGCCCGTTC[C/A]
ACTCTAGCAACTTCCACCAGGGCGCTAGCGGCAGTCCGAACCACCAGGGAGGCCAGCCCAACCGTGGTGCAGCTCCACGCCCACCAATGGCACCAGCACA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.70%	1.40%	7.79%	50.15%	NA
All Indica	2759	10.40%	2.30%	8.99%	78.36%	NA
All Japonica	1512	98.10%	0.00%	0.20%	1.72%	NA
Aus	269	25.70%	0.70%	40.15%	33.46%	NA
Indica I	595	10.60%	0.00%	5.71%	83.70%	NA
Indica II	465	14.40%	10.30%	21.29%	53.98%	NA
Indica III	913	4.50%	0.40%	3.50%	91.57%	NA
Indica Intermediate	786	14.60%	1.40%	10.56%	73.41%	NA
Temperate Japonica	767	99.00%	0.00%	0.00%	1.04%	NA
Tropical Japonica	504	97.00%	0.00%	0.60%	2.38%	NA
Japonica Intermediate	241	97.50%	0.00%	0.00%	2.49%	NA
VI/Aromatic	96	27.10%	1.00%	5.21%	66.67%	NA
Intermediate	90	64.40%	0.00%	4.44%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0136579687	G -> T	LOC_Os01g63120.1	missense_variant ; p.His304Asn; MODERATE	nonsynonymous_codon ; H304N	Average:13.33; most accessible tissue: Callus, score: 26.075	benign	-0.538	TOLERATED	1.00
vg0136579687	G -> DEL	LOC_Os01g63120.1	N	frameshift_variant	Average:13.33; most accessible tissue: Callus, score: 26.075	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0136579687	NA	2.87E-08	mr1877	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
vg0136579687	4.31E-06	2.46E-08	mr1877_2	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