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Detailed information for vg0423665696:

Variant ID: vg0423665696 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 23665696
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGGCGGATGCCAGGCGATACTGGTCAACGACGTCGCCATAATGACGACGATGATGGAGACCGGCGCCGAGACAACAGTGGGAGACGACGACAGGATTCT[C/T]
GAGAGCCAGGCCGACATCCTCGTAATCGTACGCCGGAACCAAGCGGCCCATCGTCATCGTCATCATCCTCGTCTTCCTCATCATCAGACAGACATCTACG

Reverse complement sequence

CGTAGATGTCTGTCTGATGATGAGGAAGACGAGGATGATGACGATGACGATGGGCCGCTTGGTTCCGGCGTACGATTACGAGGATGTCGGCCTGGCTCTC[G/A]
AGAATCCTGTCGTCGTCTCCCACTGTTGTCTCGGCGCCGGTCTCCATCATCGTCGTCATTATGGCGACGTCGTTGACCAGTATCGCCTGGCATCCGCCGT

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	92.90%	5.40%	1.42%	0.32%	NA
All Indica	2759	98.50%	0.90%	0.47%	0.11%	NA
All Japonica	1512	91.30%	7.60%	0.99%	0.07%	NA
Aus	269	45.40%	37.50%	13.01%	4.09%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	98.70%	1.10%	0.22%	0.00%	NA
Indica III	913	98.40%	0.90%	0.44%	0.33%	NA
Indica Intermediate	786	97.50%	1.70%	0.89%	0.00%	NA
Temperate Japonica	767	99.60%	0.00%	0.39%	0.00%	NA
Tropical Japonica	504	77.60%	20.20%	1.98%	0.20%	NA
Japonica Intermediate	241	93.80%	5.40%	0.83%	0.00%	NA
VI/Aromatic	96	93.80%	5.20%	1.04%	0.00%	NA
Intermediate	90	90.00%	6.70%	3.33%	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
vg0423665696	C -> DEL	LOC_Os04g39710.1	N	frameshift_variant	Average:36.47; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0423665696	C -> T	LOC_Os04g39710.1	stop_gained ; p.Arg353*; HIGH	stop_gained	Average:36.47; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0423665696	NA	2.19E-07	mr1227	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
vg0423665696	1.80E-06	1.80E-06	mr1362	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
vg0423665696	NA	1.10E-06	mr1830	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
vg0423665696	NA	5.73E-09	mr1852	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
vg0423665696	NA	1.29E-07	mr1077_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