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Detailed information for vg0600114214:

Variant ID: vg0600114214 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 114214
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATGATGGCGGAGGCAAGCCGGCAACGATGAAGTCAGGGAACGGAGAAACAGCTTCGCACTCCAGCCGGTCTATCCATGTGGTAGCATGCGACGTCTGCC[C/T]
AGCTCGTTGGTTTGACTCTGTCGACTCGTCCTCCTGGCGACGTGCCTCTGTGCATTTAGATCAGGCACTCGTGTACAGCTCGGACAGAGGTGGATTGATC

Reverse complement sequence

GATCAATCCACCTCTGTCCGAGCTGTACACGAGTGCCTGATCTAAATGCACAGAGGCACGTCGCCAGGAGGACGAGTCGACAGAGTCAAACCAACGAGCT[G/A]
GGCAGACGTCGCATGCTACCACATGGATAGACCGGCTGGAGTGCGAAGCTGTTTCTCCGTTCCCTGACTTCATCGTTGCCGGCTTGCCTCCGCCATCATC

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	45.80%	0.10%	27.70%	26.36%	NA
All Indica	2759	18.60%	0.10%	39.76%	41.57%	NA
All Japonica	1512	98.40%	0.00%	0.53%	1.06%	NA
Aus	269	27.50%	0.70%	50.19%	21.56%	NA
Indica I	595	9.90%	0.20%	33.95%	55.97%	NA
Indica II	465	29.90%	0.00%	31.61%	38.49%	NA
Indica III	913	16.20%	0.00%	48.19%	35.60%	NA
Indica Intermediate	786	21.10%	0.30%	39.19%	39.44%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	96.40%	0.00%	1.19%	2.38%	NA
Japonica Intermediate	241	97.50%	0.00%	0.83%	1.66%	NA
VI/Aromatic	96	33.30%	1.00%	54.17%	11.46%	NA
Intermediate	90	65.60%	0.00%	18.89%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0600114214	C -> T	LOC_Os06g01120.1	upstream_gene_variant ; 4061.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0600114214	C -> T	LOC_Os06g01130.1	upstream_gene_variant ; 321.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0600114214	C -> T	LOC_Os06g01130-LOC_Os06g01140	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0600114214	C -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0600114214	4.25E-06	5.81E-06	mr1004	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
vg0600114214	1.18E-06	NA	mr1005	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