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Detailed information for vg0137835203:

Variant ID: vg0137835203 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 37835203
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, G: 0.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

GTGGAGTTTCTTGGATGTTTTTTATTATGTAGATTTCTCACTGAATTGTATCCACAATATAGGGGCTTGGCATGCTCACGCTATCACCGGTTCTTGTACC[T/G]
CATCAACAAGCAGAATCTGGAGATAATGCAGATAATAATGCATCCTCCAGTATGGACATTCATGTAGCTTTCTTCTACTTGTCCCTGTATATCGTGGCCT

Reverse complement sequence

AGGCCACGATATACAGGGACAAGTAGAAGAAAGCTACATGAATGTCCATACTGGAGGATGCATTATTATCTGCATTATCTCCAGATTCTGCTTGTTGATG[A/C]
GGTACAAGAACCGGTGATAGCGTGAGCATGCCAAGCCCCTATATTGTGGATACAATTCAGTGAGAAATCTACATAATAAAAAACATCCAAGAAACTCCAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.20%	41.40%	0.08%	0.32%	NA
All Indica	2759	33.40%	65.90%	0.14%	0.51%	NA
All Japonica	1512	97.90%	2.10%	0.00%	0.07%	NA
Aus	269	71.00%	29.00%	0.00%	0.00%	NA
Indica I	595	37.30%	62.20%	0.00%	0.50%	NA
Indica II	465	15.30%	83.70%	0.22%	0.86%	NA
Indica III	913	42.30%	57.40%	0.00%	0.33%	NA
Indica Intermediate	786	30.90%	68.20%	0.38%	0.51%	NA
Temperate Japonica	767	97.90%	2.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.00%	2.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.10%	0.00%	0.41%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	71.10%	28.90%	0.00%	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
vg0137835203	T -> G	LOC_Os01g65200.3	synonymous_variant ; p.Pro124Pro; LOW	synonymous_codon	Average:60.72; most accessible tissue: Zhenshan97 young leaf, score: 80.056	N	N	N	N
vg0137835203	T -> G	LOC_Os01g65200.1	synonymous_variant ; p.Pro124Pro; LOW	synonymous_codon	Average:60.72; most accessible tissue: Zhenshan97 young leaf, score: 80.056	N	N	N	N
vg0137835203	T -> G	LOC_Os01g65200.2	synonymous_variant ; p.Pro124Pro; LOW	synonymous_codon	Average:60.72; most accessible tissue: Zhenshan97 young leaf, score: 80.056	N	N	N	N
vg0137835203	T -> DEL	LOC_Os01g65200.3	N	frameshift_variant	Average:60.72; most accessible tissue: Zhenshan97 young leaf, score: 80.056	N	N	N	N
vg0137835203	T -> DEL	LOC_Os01g65200.1	N	frameshift_variant	Average:60.72; most accessible tissue: Zhenshan97 young leaf, score: 80.056	N	N	N	N
vg0137835203	T -> DEL	LOC_Os01g65200.2	N	frameshift_variant	Average:60.72; most accessible tissue: Zhenshan97 young leaf, score: 80.056	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0137835203	2.16E-08	1.31E-25	mr1375	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
vg0137835203	NA	7.85E-08	mr1375	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
vg0137835203	4.72E-19	NA	mr1517	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
vg0137835203	3.70E-15	1.39E-18	mr1517	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
vg0137835203	3.11E-17	2.39E-72	mr1538	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
vg0137835203	2.36E-10	5.42E-13	mr1538	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
vg0137835203	1.17E-25	NA	mr1517_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
vg0137835203	3.28E-20	2.21E-21	mr1517_2	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
vg0137835203	1.78E-19	NA	mr1538_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
vg0137835203	2.24E-12	1.95E-18	mr1538_2	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