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Detailed information for vg0401293916:

Variant ID: vg0401293916 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1293916
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTCTTCCAAGGACCAATCTGGATATGACTCTATTTGGGTTGTTATCGACCGCCAAACCAAAGTTGCATATTTCATCGCAGTCAAAACCACTTATCCCGG[C/T]
AGTAAGTTGGCAGAATTATACTTTGCTAGGATAGTTTGTCTTCATGGAGTACCGAAGAGAATCGTCTCCGATCGGGGTAGCCAATTCACTACTAAGTTCT

Reverse complement sequence

AGAACTTAGTAGTGAATTGGCTACCCCGATCGGAGACGATTCTCTTCGGTACTCCATGAAGACAAACTATCCTAGCAAAGTATAATTCTGCCAACTTACT[G/A]
CCGGGATAAGTGGTTTTGACTGCGATGAAATATGCAACTTTGGTTTGGCGGTCGATAACAACCCAAATAGAGTCATATCCAGATTGGTCCTTGGAAGACC

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	46.80%	7.60%	2.96%	42.64%	NA
All Indica	2759	45.10%	7.30%	1.34%	46.28%	NA
All Japonica	1512	55.80%	1.10%	0.79%	42.33%	NA
Aus	269	22.70%	45.40%	31.60%	0.37%	NA
Indica I	595	74.50%	0.00%	0.17%	25.38%	NA
Indica II	465	29.00%	3.40%	1.72%	65.81%	NA
Indica III	913	33.70%	13.90%	1.31%	51.04%	NA
Indica Intermediate	786	45.50%	7.40%	2.04%	45.04%	NA
Temperate Japonica	767	55.90%	1.30%	1.17%	41.59%	NA
Tropical Japonica	504	66.70%	0.20%	0.20%	32.94%	NA
Japonica Intermediate	241	32.80%	2.10%	0.83%	64.32%	NA
VI/Aromatic	96	11.50%	13.50%	4.17%	70.83%	NA
Intermediate	90	56.70%	8.90%	2.22%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401293916	C -> DEL	LOC_Os04g03110.1	N	frameshift_variant	Average:13.692; most accessible tissue: Callus, score: 38.569	N	N	N	N
vg0401293916	C -> T	LOC_Os04g03110.1	missense_variant&splice_region_variant ; p.Ala1113Val; MODERATE	nonsynonymous_codon ; A1113V	Average:13.692; most accessible tissue: Callus, score: 38.569	unknown	unknown	TOLERATED	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401293916	2.28E-08	NA	mr1549	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
vg0401293916	NA	4.99E-11	mr1612	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
vg0401293916	1.58E-07	2.20E-36	mr1757	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
vg0401293916	2.52E-07	NA	mr1549_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
vg0401293916	6.36E-06	8.48E-28	mr1757_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