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Detailed information for vg0313544485:

Variant ID: vg0313544485 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 13544485
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACAGACCGAGCGTCTAAACCAGATCCTAGAAGATATGCTCCGCGCATGTGTACTAGATTTCGGGAAGACCTGGGATAAGAGCCTCCCCTATGCCGAGTT[T/C]
TCCTACAACAACAGCTATCAAGCCAGCATACAAATGGCACCGTATGAAGCGTTGTACGGGCGCAAATGCCGGACACCGCTATTGTGGGACCAAGTTGGAG

Reverse complement sequence

CTCCAACTTGGTCCCACAATAGCGGTGTCCGGCATTTGCGCCCGTACAACGCTTCATACGGTGCCATTTGTATGCTGGCTTGATAGCTGTTGTTGTAGGA[A/G]
AACTCGGCATAGGGGAGGCTCTTATCCCAGGTCTTCCCGAAATCTAGTACACATGCGCGGAGCATATCTTCTAGGATCTGGTTTAGACGCTCGGTCTGTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.30%	0.30%	31.61%	12.74%	NA
All Indica	2759	43.50%	0.30%	43.02%	13.16%	NA
All Japonica	1512	81.30%	0.00%	7.01%	11.71%	NA
Aus	269	28.60%	2.60%	55.02%	13.75%	NA
Indica I	595	66.40%	0.20%	18.66%	14.79%	NA
Indica II	465	51.80%	0.00%	33.76%	14.41%	NA
Indica III	913	21.50%	0.40%	67.14%	10.95%	NA
Indica Intermediate	786	46.80%	0.50%	38.93%	13.74%	NA
Temperate Japonica	767	96.70%	0.00%	0.65%	2.61%	NA
Tropical Japonica	504	65.10%	0.00%	14.29%	20.63%	NA
Japonica Intermediate	241	66.00%	0.00%	12.03%	21.99%	NA
VI/Aromatic	96	51.00%	0.00%	32.29%	16.67%	NA
Intermediate	90	65.60%	0.00%	24.44%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0313544485	T -> C	LOC_Os03g23860.1	synonymous_variant ; p.Phe1536Phe; LOW	synonymous_codon	Average:37.546; most accessible tissue: Minghui63 young leaf, score: 62.741	N	N	N	N
vg0313544485	T -> DEL	LOC_Os03g23860.1	N	frameshift_variant	Average:37.546; most accessible tissue: Minghui63 young leaf, score: 62.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0313544485	4.70E-07	NA	mr1018	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
vg0313544485	1.04E-06	NA	mr1019	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
vg0313544485	NA	3.20E-20	mr1010_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
vg0313544485	NA	2.59E-06	mr1695_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
vg0313544485	NA	1.65E-11	mr1844_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