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Detailed information for vg0211794496:

Variant ID: vg0211794496 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 11794496
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGGTGTCGTACTCCGCTCTTCTAGGATCAGACAGGGGAACACCAGTTGTTTGGTACAGAAGTTTTAAATGAGGCAGAAGAGAAAGTCAGAGCTGTCAGG[G/C]
AAAGATTGAGAATCGCGCAATCTCGACAAAGAAGCTATGCAGACAACCGCCGAAGGGAGCTCGTTTTCCAAGCAGGGGATTATGTGTATCTCCGTGTCAC

Reverse complement sequence

GTGACACGGAGATACACATAATCCCCTGCTTGGAAAACGAGCTCCCTTCGGCGGTTGTCTGCATAGCTTCTTTGTCGAGATTGCGCGATTCTCAATCTTT[C/G]
CCTGACAGCTCTGACTTTCTCTTCTGCCTCATTTAAAACTTCTGTACCAAACAACTGGTGTTCCCCTGTCTGATCCTAGAAGAGCGGAGTACGACACCTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.50%	0.60%	1.50%	2.48%	NA
All Indica	2759	93.10%	0.90%	2.32%	3.70%	NA
All Japonica	1512	99.50%	0.00%	0.20%	0.33%	NA
Aus	269	95.20%	0.40%	1.12%	3.35%	NA
Indica I	595	96.60%	0.80%	1.85%	0.67%	NA
Indica II	465	93.10%	1.30%	2.80%	2.80%	NA
Indica III	913	90.80%	1.00%	1.64%	6.57%	NA
Indica Intermediate	786	93.00%	0.60%	3.18%	3.18%	NA
Temperate Japonica	767	99.60%	0.00%	0.13%	0.26%	NA
Tropical Japonica	504	99.40%	0.00%	0.20%	0.40%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0211794496	G -> DEL	LOC_Os02g20020.1	N	frameshift_variant	Average:14.719; most accessible tissue: Callus, score: 25.596	N	N	N	N
vg0211794496	G -> C	LOC_Os02g20020.1	missense_variant ; p.Glu1078Gln; MODERATE	nonsynonymous_codon ; E1078Q	Average:14.719; most accessible tissue: Callus, score: 25.596	possibly damaging	1.705	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0211794496	1.07E-06	1.07E-06	mr1396	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