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Detailed information for vg1112971005:

Variant ID: vg1112971005 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12971005
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGGTGCTATCTTCATCTTCAGGGTAGTTGTGAACTCCATAGTCTTGACCATGTGGCTTGTGTGGATGATACTAAAAAGCTGATGACTCTAACTCCTCAT[C/G]
AAAGCGATGACGTAGCTCTCCAATGGCCACCAAGGCTGCCTCCTGACAAGCATGACTATACTTTTTTCCCCCAGCTTCAAACTTTATTGACGGAAGGTCT

Reverse complement sequence

AGACCTTCCGTCAATAAAGTTTGAAGCTGGGGGAAAAAAGTATAGTCATGCTTGTCAGGAGGCAGCCTTGGTGGCCATTGGAGAGCTACGTCATCGCTTT[G/C]
ATGAGGAGTTAGAGTCATCAGCTTTTTAGTATCATCCACACAAGCCACATGGTCAAGACTATGGAGTTCACAACTACCCTGAAGATGAAGATAGCACCAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.60%	1.90%	1.97%	6.47%	NA
All Indica	2759	83.80%	3.00%	3.30%	9.86%	NA
All Japonica	1512	98.00%	0.40%	0.00%	1.59%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	96.60%	0.50%	1.34%	1.51%	NA
Indica II	465	85.60%	0.90%	1.08%	12.47%	NA
Indica III	913	69.30%	6.40%	5.48%	18.84%	NA
Indica Intermediate	786	89.90%	2.30%	3.56%	4.20%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	95.80%	0.00%	0.00%	4.17%	NA
Japonica Intermediate	241	97.90%	0.80%	0.00%	1.24%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	87.80%	2.20%	1.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112971005	C -> DEL	LOC_Os11g22560.1	N	frameshift_variant	Average:14.7; most accessible tissue: Callus, score: 50.537	N	N	N	N
vg1112971005	C -> G	LOC_Os11g22560.1	missense_variant ; p.Asp157His; MODERATE	nonsynonymous_codon ; D157H	Average:14.7; most accessible tissue: Callus, score: 50.537	unknown	unknown	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112971005	2.82E-06	2.82E-06	mr1655	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