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Detailed information for vg0103158278:

Variant ID: vg0103158278 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3158278
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GCTCGCCAGATGAACGAGTTGATGGAGAAGACGTCCCGTTACCTTGCTGAGTTCGGGACGGGTGGTCGCTATCTCCAACTTAACTCTGTGAGTTCGGCGA[C/G]
TGACGAATTGCCGACGCTGGAGCTTCCAAAGTCCACGCCCACTGAACGCCGCAACGCCCGCATGGTGGAGGAGGATCTATTTAGCATCCAAGATTGTTTG

Reverse complement sequence

CAAACAATCTTGGATGCTAAATAGATCCTCCTCCACCATGCGGGCGTTGCGGCGTTCAGTGGGCGTGGACTTTGGAAGCTCCAGCGTCGGCAATTCGTCA[G/C]
TCGCCGAACTCACAGAGTTAAGTTGGAGATAGCGACCACCCGTCCCGAACTCAGCAAGGTAACGGGACGTCTTCTCCATCAACTCGTTCATCTGGCGAGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.10%	0.30%	2.01%	4.63%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	78.50%	0.90%	6.22%	14.42%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	85.40%	0.10%	2.74%	11.73%	NA
Tropical Japonica	504	70.00%	0.60%	5.36%	24.01%	NA
Japonica Intermediate	241	74.30%	3.70%	19.09%	2.90%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	98.90%	0.00%	1.11%	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
vg0103158278	C -> G	LOC_Os01g06690.1	missense_variant ; p.Thr285Ser; MODERATE	nonsynonymous_codon ; T285S	Average:19.294; most accessible tissue: Callus, score: 36.976	unknown	unknown	DELETERIOUS	0.00
vg0103158278	C -> DEL	LOC_Os01g06690.1	N	frameshift_variant	Average:19.294; most accessible tissue: Callus, score: 36.976	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103158278	NA	1.42E-06	mr1114	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
vg0103158278	NA	7.68E-08	mr1117	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
vg0103158278	NA	4.66E-07	mr1118	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
vg0103158278	7.04E-06	5.07E-09	mr1123	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
vg0103158278	NA	9.97E-06	mr1150	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
vg0103158278	NA	5.77E-07	mr1240	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
vg0103158278	NA	8.52E-09	mr1242	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
vg0103158278	NA	8.09E-08	mr1247	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
vg0103158278	NA	4.63E-07	mr1496	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
vg0103158278	3.47E-07	4.77E-07	mr1682	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
vg0103158278	NA	3.71E-07	mr1693	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
vg0103158278	NA	1.17E-06	mr1917	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
vg0103158278	NA	8.85E-07	mr1961	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
vg0103158278	NA	5.85E-06	mr1119_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