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Detailed information for vg0113688544:

Variant ID: vg0113688544 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13688544
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGTATGGTTGATGGCTCCGATTGCTTTGATGTTTGACCAAATCTCTTTCTACGAGATGATCTTGGTCTTTTTGAATCACAAGTTTGATTATCAAATCG[C/T]
TGACCGGCTAATCCTTTCTTGTACTTAGCCATAAGCATCTCAAAAGTGAGCTTCGGCTTTTTGGTCTTTTGGGAACTAGATGACTCATCCTTGGCAATTT

Reverse complement sequence

AAATTGCCAAGGATGAGTCATCTAGTTCCCAAAAGACCAAAAAGCCGAAGCTCACTTTTGAGATGCTTATGGCTAAGTACAAGAAAGGATTAGCCGGTCA[G/A]
CGATTTGATAATCAAACTTGTGATTCAAAAAGACCAAGATCATCTCGTAGAAAGAGATTTGGTCAAACATCAAAGCAATCGGAGCCATCAACCATACCAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.20%	13.10%	32.99%	11.68%	NA
All Indica	2759	20.10%	17.80%	45.81%	16.27%	NA
All Japonica	1512	86.90%	0.90%	7.54%	4.70%	NA
Aus	269	13.00%	31.60%	46.47%	8.92%	NA
Indica I	595	29.60%	3.70%	33.78%	32.94%	NA
Indica II	465	25.60%	28.00%	29.68%	16.77%	NA
Indica III	913	8.80%	19.80%	61.77%	9.64%	NA
Indica Intermediate	786	22.90%	20.10%	45.93%	11.07%	NA
Temperate Japonica	767	98.30%	0.10%	0.65%	0.91%	NA
Tropical Japonica	504	66.50%	2.20%	19.44%	11.90%	NA
Japonica Intermediate	241	93.40%	0.40%	4.56%	1.66%	NA
VI/Aromatic	96	47.90%	19.80%	32.29%	0.00%	NA
Intermediate	90	50.00%	13.30%	27.78%	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
vg0113688544	C -> T	LOC_Os01g24294.1	synonymous_variant ; p.Gln1289Gln; LOW	synonymous_codon	Average:21.403; most accessible tissue: Minghui63 young leaf, score: 48.378	N	N	N	N
vg0113688544	C -> DEL	LOC_Os01g24294.1	N	frameshift_variant	Average:21.403; most accessible tissue: Minghui63 young leaf, score: 48.378	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113688544	NA	9.45E-06	mr1188	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
vg0113688544	2.70E-06	NA	mr1296	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
vg0113688544	NA	4.00E-06	mr1602	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
vg0113688544	NA	3.78E-06	mr1754_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