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Detailed information for vg0315353447:

Variant ID: vg0315353447 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15353447
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

CAAAGAATAAAGTCCATGGCACAATTTCAACCGAGCCGATTGAATCATCACCATGTTCCACAATAAAATCGGCTATAGCTTGTCCCTTAATCGCCTTCAG[T/C]
GACTCATACCGAAGATCAAACTCAGTTAAGGAAAATATCCACTTTTCAACCCTTCCTTTCAATATTGGAGCCGATAACATGTATTTGACAACATCGGCCT

Reverse complement sequence

AGGCCGATGTTGTCAAATACATGTTATCGGCTCCAATATTGAAAGGAAGGGTTGAAAAGTGGATATTTTCCTTAACTGAGTTTGATCTTCGGTATGAGTC[A/G]
CTGAAGGCGATTAAGGGACAAGCTATAGCCGATTTTATTGTGGAACATGGTGATGATTCAATCGGCTCGGTTGAAATTGTGCCATGGACTTTATTCTTTG

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	81.00%	17.60%	0.85%	0.55%	NA
All Indica	2759	97.00%	0.90%	1.23%	0.94%	NA
All Japonica	1512	47.00%	52.70%	0.33%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.00%	0.30%	0.67%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	93.80%	1.90%	2.08%	2.30%	NA
Indica Intermediate	786	97.70%	0.40%	1.27%	0.64%	NA
Temperate Japonica	767	15.60%	84.40%	0.00%	0.00%	NA
Tropical Japonica	504	81.90%	17.30%	0.79%	0.00%	NA
Japonica Intermediate	241	73.40%	26.10%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	14.40%	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
vg0315353447	T -> C	LOC_Os03g26890.1	synonymous_variant ; p.Ser894Ser; LOW	synonymous_codon	Average:36.8; most accessible tissue: Minghui63 flag leaf, score: 53.617	N	N	N	N
vg0315353447	T -> DEL	LOC_Os03g26890.1	N	frameshift_variant	Average:36.8; most accessible tissue: Minghui63 flag leaf, score: 53.617	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315353447	2.23E-06	2.74E-21	mr1155	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
vg0315353447	NA	4.46E-06	mr1330	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
vg0315353447	NA	6.73E-07	mr1543	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
vg0315353447	NA	2.19E-06	mr1815	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
vg0315353447	NA	4.44E-13	mr1844	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
vg0315353447	NA	6.15E-06	mr1844	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
vg0315353447	NA	2.48E-14	mr1182_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
vg0315353447	NA	1.32E-06	mr1182_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
vg0315353447	NA	7.89E-11	mr1282_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
vg0315353447	NA	5.49E-07	mr1308_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
vg0315353447	NA	1.60E-07	mr1399_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
vg0315353447	NA	2.83E-09	mr1584_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
vg0315353447	NA	3.36E-12	mr1853_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
vg0315353447	NA	3.91E-06	mr1853_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