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Detailed information for vg0232442595:

Variant ID: vg0232442595 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 32442595
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACGCTATACCACGTTGCAACAGGCCCAACCATCCACCTATACTATTCAATTCCAAAAGACTAGTCTAGGGTGAGTCTAATCACGGTGAATCTGGTTGAC[C/T]
GCCCATAACCGCGGGCACGGCTATTCGAATAGTTTTACTCCGATCAGAGGTGTACAACTGTACCAACAAGACACAGCCCCACGACATGTTTCCATGCGCC

Reverse complement sequence

GGCGCATGGAAACATGTCGTGGGGCTGTGTCTTGTTGGTACAGTTGTACACCTCTGATCGGAGTAAAACTATTCGAATAGCCGTGCCCGCGGTTATGGGC[G/A]
GTCAACCAGATTCACCGTGATTAGACTCACCCTAGACTAGTCTTTTGGAATTGAATAGTATAGGTGGATGGTTGGGCCTGTTGCAACGTGGTATAGCGTT

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	52.70%	0.20%	6.88%	40.18%	NA
All Indica	2759	29.20%	0.20%	8.48%	62.05%	NA
All Japonica	1512	99.10%	0.00%	0.26%	0.66%	NA
Aus	269	35.70%	1.90%	20.07%	42.38%	NA
Indica I	595	21.50%	0.00%	5.04%	73.45%	NA
Indica II	465	27.70%	0.40%	8.82%	63.01%	NA
Indica III	913	37.30%	0.20%	10.08%	52.35%	NA
Indica Intermediate	786	26.60%	0.30%	9.03%	64.12%	NA
Temperate Japonica	767	99.50%	0.00%	0.13%	0.39%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	95.90%	0.00%	1.24%	2.90%	NA
VI/Aromatic	96	29.20%	0.00%	31.25%	39.58%	NA
Intermediate	90	68.90%	0.00%	3.33%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0232442595	C -> T	LOC_Os02g53010.1	downstream_gene_variant ; 267.0bp to feature; MODIFIER	silent_mutation	Average:9.928; most accessible tissue: Callus, score: 22.161	N	N	N	N
vg0232442595	C -> T	LOC_Os02g53010-LOC_Os02g53020	intergenic_region ; MODIFIER	silent_mutation	Average:9.928; most accessible tissue: Callus, score: 22.161	N	N	N	N
vg0232442595	C -> DEL	N	N	silent_mutation	Average:9.928; most accessible tissue: Callus, score: 22.161	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0232442595	3.96E-06	NA	mr1044	Ind_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
vg0232442595	NA	5.26E-08	mr1188	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
vg0232442595	NA	7.80E-06	mr1948	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