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Detailed information for vg0401972146:

Variant ID: vg0401972146 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 1972146
Reference Allele: CTGTAGCATCACATAGGCTAATCA	Alternative Allele: TTGTAGCATCACATAGGCTAATCA,C
Primary Allele: CTGTAGCATCACATAGGCTA ATCA	Secondary Allele: TTGTAGCATCACATAGGCTA ATCA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTAAACATATACTAATAAAAAAAACTAATTTCATAAATGAGAACTAATCCAGGAGGCGAATTTTTTAAGCCTAATTAATCCATAATTAGCAAATCTTTA[CTGTAGCATCACATAGGCTAATCA/TTGTAGCATCACATAGGCTAATCA,C]
TGTATTAATTAGGCTCAAAAGATTTGTCTCGCGAATTAGTCCAAGGTTATGAAATGTATTTTATAATTAATCTATGTTTAATACTCTAAATTTGCGTCCA

Reverse complement sequence

TGGACGCAAATTTAGAGTATTAAACATAGATTAATTATAAAATACATTTCATAACCTTGGACTAATTCGCGAGACAAATCTTTTGAGCCTAATTAATACA[TGATTAGCCTATGTGATGCTACAG/TGATTAGCCTATGTGATGCTACAA,G]
TAAAGATTTGCTAATTATGGATTAATTAGGCTTAAAAAATTCGCCTCCTGGATTAGTTCTCATTTATGAAATTAGTTTTTTTTATTAGTATATGTTTAAT

Allele Frequencies:

Populations	Population Size	Frequency of CTGTAGCATCACATAGGCTA ATCA(primary allele)	Frequency of TTGTAGCATCACATAGGCTA ATCA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.00%	12.50%	0.89%	47.02%	C: 0.61%
All Indica	2759	27.60%	0.80%	0.33%	71.26%	NA
All Japonica	1512	47.10%	36.30%	1.85%	12.90%	C: 1.85%
Aus	269	92.90%	0.00%	0.00%	7.06%	NA
Indica I	595	13.90%	0.00%	0.17%	85.88%	NA
Indica II	465	30.80%	0.20%	0.43%	68.60%	NA
Indica III	913	33.50%	1.00%	0.44%	65.06%	NA
Indica Intermediate	786	29.30%	1.50%	0.25%	68.96%	NA
Temperate Japonica	767	51.40%	42.90%	1.69%	0.52%	C: 3.52%
Tropical Japonica	504	36.90%	24.20%	2.98%	35.91%	NA
Japonica Intermediate	241	54.80%	40.70%	0.00%	4.15%	C: 0.41%
VI/Aromatic	96	87.50%	10.40%	0.00%	2.08%	NA
Intermediate	90	37.80%	11.10%	5.56%	44.44%	C: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401972146	CTGTAGCATCACATAGGCTAATCA -> C	LOC_Os04g04220.1	upstream_gene_variant ; 3102.0bp to feature; MODIFIER	silent_mutation	Average:36.612; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0401972146	CTGTAGCATCACATAGGCTAATCA -> C	LOC_Os04g04230.1	downstream_gene_variant ; 474.0bp to feature; MODIFIER	silent_mutation	Average:36.612; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0401972146	CTGTAGCATCACATAGGCTAATCA -> C	LOC_Os04g04240.1	downstream_gene_variant ; 2533.0bp to feature; MODIFIER	silent_mutation	Average:36.612; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0401972146	CTGTAGCATCACATAGGCTAATCA -> C	LOC_Os04g04230-LOC_Os04g04240	intergenic_region ; MODIFIER	silent_mutation	Average:36.612; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0401972146	CTGTAGCATCACATAGGCTAATCA -> DEL	N	N	silent_mutation	Average:36.612; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0401972146	CTGTAGCATCACATAGGCTAATCA -> TTGTAGCATCACATAGGCTAATCA	LOC_Os04g04220.1	upstream_gene_variant ; 3101.0bp to feature; MODIFIER	silent_mutation	Average:36.612; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0401972146	CTGTAGCATCACATAGGCTAATCA -> TTGTAGCATCACATAGGCTAATCA	LOC_Os04g04230.1	downstream_gene_variant ; 473.0bp to feature; MODIFIER	silent_mutation	Average:36.612; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0401972146	CTGTAGCATCACATAGGCTAATCA -> TTGTAGCATCACATAGGCTAATCA	LOC_Os04g04240.1	downstream_gene_variant ; 2534.0bp to feature; MODIFIER	silent_mutation	Average:36.612; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0401972146	CTGTAGCATCACATAGGCTAATCA -> TTGTAGCATCACATAGGCTAATCA	LOC_Os04g04230-LOC_Os04g04240	intergenic_region ; MODIFIER	silent_mutation	Average:36.612; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401972146	6.87E-07	NA	mr1037_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
vg0401972146	7.76E-13	NA	mr1798_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
vg0401972146	5.54E-07	3.62E-09	mr1798_2	Ind_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
vg0401972146	1.82E-06	2.48E-08	mr1798_2	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