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Detailed information for vg1223993351:

Variant ID: vg1223993351 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 23993351
Reference Allele: CGCTAGCTA	Alternative Allele: TGCTAGCTA,C
Primary Allele: CGCTAGCTA	Secondary Allele: TGCTAGCTA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATATCGCAATTTACAGGTGGATTTTATAATTTGTTTTGTTATTAGGCTACGTTAAATACTTCAAACGTATATCCGATGTGACACGGCAAAAATTTTTAC[CGCTAGCTA/TGCTAGCTA,C]
GCTGGATCTAAACACAGCGTTAACCATATAAAATTCCACAAAACTCCTACCCCCCCCCCCCCCCCCCGCGTTCTACTAATCGCAGTCGCATCCAAAGGTT

Reverse complement sequence

AACCTTTGGATGCGACTGCGATTAGTAGAACGCGGGGGGGGGGGGGGGGGGTAGGAGTTTTGTGGAATTTTATATGGTTAACGCTGTGTTTAGATCCAGC[TAGCTAGCG/TAGCTAGCA,G]
GTAAAAATTTTTGCCGTGTCACATCGGATATACGTTTGAAGTATTTAACGTAGCCTAATAACAAAACAAATTATAAAATCCACCTGTAAATTGCGATATG

Allele Frequencies:

Populations	Population Size	Frequency of CGCTAGCTA(primary allele)	Frequency of TGCTAGCTA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.30%	6.50%	0.51%	33.64%	C: 0.08%
All Indica	2759	48.10%	3.60%	0.76%	47.52%	C: 0.07%
All Japonica	1512	89.20%	10.20%	0.07%	0.53%	NA
Aus	269	8.20%	1.10%	0.74%	89.96%	NA
Indica I	595	55.60%	1.00%	0.50%	42.86%	NA
Indica II	465	70.80%	2.60%	0.43%	26.02%	C: 0.22%
Indica III	913	31.30%	3.20%	0.66%	64.84%	NA
Indica Intermediate	786	48.30%	6.60%	1.27%	43.64%	C: 0.13%
Temperate Japonica	767	90.20%	9.30%	0.13%	0.39%	NA
Tropical Japonica	504	94.60%	4.60%	0.00%	0.79%	NA
Japonica Intermediate	241	74.70%	24.90%	0.00%	0.41%	NA
VI/Aromatic	96	45.80%	44.80%	0.00%	9.38%	NA
Intermediate	90	68.90%	6.70%	0.00%	22.22%	C: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1223993351	CGCTAGCTA -> TGCTAGCTA	LOC_Os12g39010.1	upstream_gene_variant ; 381.0bp to feature; MODIFIER	silent_mutation	Average:44.713; most accessible tissue: Minghui63 root, score: 85.669	N	N	N	N
vg1223993351	CGCTAGCTA -> TGCTAGCTA	LOC_Os12g39000-LOC_Os12g39010	intergenic_region ; MODIFIER	silent_mutation	Average:44.713; most accessible tissue: Minghui63 root, score: 85.669	N	N	N	N
vg1223993351	CGCTAGCTA -> DEL	N	N	silent_mutation	Average:44.713; most accessible tissue: Minghui63 root, score: 85.669	N	N	N	N
vg1223993351	CGCTAGCTA -> C	LOC_Os12g39010.1	upstream_gene_variant ; 380.0bp to feature; MODIFIER	silent_mutation	Average:44.713; most accessible tissue: Minghui63 root, score: 85.669	N	N	N	N
vg1223993351	CGCTAGCTA -> C	LOC_Os12g39000-LOC_Os12g39010	intergenic_region ; MODIFIER	silent_mutation	Average:44.713; most accessible tissue: Minghui63 root, score: 85.669	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223993351	6.62E-06	6.61E-06	mr1038	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1223993351	NA	1.43E-06	mr1693	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1223993351	NA	1.87E-06	mr1745	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1223993351	4.69E-06	NA	mr1350_2	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