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Detailed information for vg0612027205:

Variant ID: vg0612027205 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 12027205
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCTTATTATGCCGTCGTTATTGGGCGTCTACGTCTTCACCGCCGGCTTGCCTTCGCCGCCGCCGACTGGTGTCTCCGCCTGCACGGCTGGCCTATTATG[C/T]
CGCCGTCTTCACTGACCGGCCGCCTTGTCTGACGCCGACTGGTTTATTTGGCTCCACGGCTGTGCGTCTTCATCATCATTGACTGGCGCCATCGTCATCG

Reverse complement sequence

CGATGACGATGGCGCCAGTCAATGATGATGAAGACGCACAGCCGTGGAGCCAAATAAACCAGTCGGCGTCAGACAAGGCGGCCGGTCAGTGAAGACGGCG[G/A]
CATAATAGGCCAGCCGTGCAGGCGGAGACACCAGTCGGCGGCGGCGAAGGCAAGCCGGCGGTGAAGACGTAGACGCCCAATAACGACGGCATAATAAGCC

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	49.70%	0.60%	1.97%	47.74%	NA
All Indica	2759	30.50%	1.00%	1.70%	66.80%	NA
All Japonica	1512	91.40%	0.10%	2.12%	6.42%	NA
Aus	269	13.80%	0.00%	3.72%	82.53%	NA
Indica I	595	7.70%	0.00%	2.18%	90.08%	NA
Indica II	465	19.10%	0.60%	2.80%	77.42%	NA
Indica III	913	53.10%	2.00%	0.99%	43.92%	NA
Indica Intermediate	786	28.10%	0.90%	1.53%	69.47%	NA
Temperate Japonica	767	98.70%	0.00%	0.00%	1.30%	NA
Tropical Japonica	504	80.20%	0.20%	5.75%	13.89%	NA
Japonica Intermediate	241	91.70%	0.00%	1.24%	7.05%	NA
VI/Aromatic	96	33.30%	0.00%	0.00%	66.67%	NA
Intermediate	90	62.20%	0.00%	4.44%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0612027205	C -> T	LOC_Os06g20830.1	intron_variant ; MODIFIER	silent_mutation	Average:9.681; most accessible tissue: Callus, score: 41.366	N	N	N	N
vg0612027205	C -> DEL	N	N	silent_mutation	Average:9.681; most accessible tissue: Callus, score: 41.366	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0612027205	2.39E-06	2.39E-06	mr1377	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