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Detailed information for vg0136578944:

Variant ID: vg0136578944 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 36578944
Reference Allele: G	Alternative Allele: T,A
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGCTGCGGTTCCCGGTGCTAAATCAATCCGGAATTCAATCTCTCTCTTGGGTGGCATGGTAGTGAGGTCTTCAGGAAACACTTCTGGATACTCACAGAC[G/T,A]
ATGGGTATATCTTCCAATTTCCTCAAGCTTTTCTCCACGGTGTCCACTGGGATTTCCGTCTCGATCTGATTCAAAGAGACCCCTTGCTTTGGTGAGTCTG

Reverse complement sequence

CAGACTCACCAAAGCAAGGGGTCTCTTTGAATCAGATCGAGACGGAAATCCCAGTGGACACCGTGGAGAAAAGCTTGAGGAAATTGGAAGATATACCCAT[C/A,T]
GTCTGTGAGTATCCAGAAGTGTTTCCTGAAGACCTCACTACCATGCCACCCAAGAGAGAGATTGAATTCCGGATTGATTTAGCACCGGGAACCGCAGCAA

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	51.20%	1.00%	5.88%	41.92%	A: 0.04%
All Indica	2759	22.90%	0.50%	8.26%	68.29%	NA
All Japonica	1512	97.40%	0.20%	0.93%	1.32%	A: 0.13%
Aus	269	81.40%	1.10%	8.55%	8.92%	NA
Indica I	595	22.90%	0.00%	3.36%	73.78%	NA
Indica II	465	44.70%	0.60%	7.53%	47.10%	NA
Indica III	913	6.50%	0.90%	10.95%	81.71%	NA
Indica Intermediate	786	29.10%	0.50%	9.29%	61.07%	NA
Temperate Japonica	767	98.00%	0.00%	0.91%	0.78%	A: 0.26%
Tropical Japonica	504	97.20%	0.20%	0.79%	1.79%	NA
Japonica Intermediate	241	95.90%	0.80%	1.24%	2.07%	NA
VI/Aromatic	96	35.40%	24.00%	8.33%	32.29%	NA
Intermediate	90	68.90%	1.10%	5.56%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0136578944	G -> T	LOC_Os01g63120.1	synonymous_variant ; p.Ile551Ile; LOW	synonymous_codon	Average:8.817; most accessible tissue: Callus, score: 38.678	N	N	N	N
vg0136578944	G -> A	LOC_Os01g63120.1	synonymous_variant ; p.Ile551Ile; LOW	synonymous_codon	Average:8.817; most accessible tissue: Callus, score: 38.678	N	N	N	N
vg0136578944	G -> DEL	LOC_Os01g63120.1	N	frameshift_variant	Average:8.817; most accessible tissue: Callus, score: 38.678	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0136578944	9.25E-06	1.07E-08	mr1115	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