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Detailed information for vg1204312140:

Variant ID: vg1204312140 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4312140
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGCAAAGACATCCAATATACCCTAGGTTTAATTCCAAATGGAGGTGGGCTATCTCCTCCGGTTATCGGCTATGATGCCCCCAAGACCTCAGCTCTTCTT[C/G]
AAGGGCTCGTCAGAGAACCAGCCGATGCCGGCAAAAAGAGGAAAACCAGATCGTCGGCTGTAAGCTTCGTAGCCCCAACTAAGAAGAAGAAGACAAAGAA

Reverse complement sequence

TTCTTTGTCTTCTTCTTCTTAGTTGGGGCTACGAAGCTTACAGCCGACGATCTGGTTTTCCTCTTTTTGCCGGCATCGGCTGGTTCTCTGACGAGCCCTT[G/C]
AAGAAGAGCTGAGGTCTTGGGGGCATCATAGCCGATAACCGGAGGAGATAGCCCACCTCCATTTGGAATTAAACCTAGGGTATATTGGATGTCTTTGCCA

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	71.70%	8.00%	6.94%	13.35%	NA
All Indica	2759	73.80%	8.00%	10.22%	8.01%	NA
All Japonica	1512	70.00%	2.10%	1.65%	26.32%	NA
Aus	269	52.40%	43.10%	3.72%	0.74%	NA
Indica I	595	67.70%	4.90%	16.30%	11.09%	NA
Indica II	465	82.20%	1.70%	7.74%	8.39%	NA
Indica III	913	70.50%	14.30%	8.54%	6.57%	NA
Indica Intermediate	786	77.10%	6.70%	9.03%	7.12%	NA
Temperate Japonica	767	87.60%	0.10%	0.78%	11.47%	NA
Tropical Japonica	504	53.60%	5.60%	2.78%	38.10%	NA
Japonica Intermediate	241	48.10%	0.80%	2.07%	48.96%	NA
VI/Aromatic	96	85.40%	3.10%	4.17%	7.29%	NA
Intermediate	90	82.20%	6.70%	7.78%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204312140	C -> DEL	LOC_Os12g08500.1	N	frameshift_variant	Average:8.829; most accessible tissue: Callus, score: 25.973	N	N	N	N
vg1204312140	C -> G	LOC_Os12g08500.1	missense_variant ; p.Gln173Glu; MODERATE	nonsynonymous_codon ; Q173E	Average:8.829; most accessible tissue: Callus, score: 25.973	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204312140	4.98E-08	7.30E-17	mr1158	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