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Detailed information for vg0112718109:

Variant ID: vg0112718109 (JBrowse)	Variation Type: INDEL
Chromosome: chr01	Position: 12718109
Reference Allele: C	Alternative Allele: T,CTGTCATACACACACAACTTTTCAATTTT,CTATCAGATCAACTTGTCATACACACACAACTTTTCAATTTT
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATAGAAAAGTTGTGTGTGTATGAAAGGTTTGATGTGATGGAAAGTTGGAAGTTTGGAAAAAAAACTTTGGAACTAAGGTTGTGTTTAGATCCAAACTTC[C/T,CTGTCATACACACACAACTTTTCAATTTT,CTATCAGATCAACTTGTCATACACACACAACTTTTCAATTTT]
AACTTTTTCTATCACATCAACCTGTCATACACACACAACTTTTCAATCACATCGTACCAATTTCAATCTAAACTTTCAACTTTAGAATGAACTAAACACA

Reverse complement sequence

TGTGTTTAGTTCATTCTAAAGTTGAAAGTTTAGATTGAAATTGGTACGATGTGATTGAAAAGTTGTGTGTGTATGACAGGTTGATGTGATAGAAAAAGTT[G/A,AAAATTGAAAAGTTGTGTGTGTATGACAG,AAAATTGAAAAGTTGTGTGTGTATGACAAGTTGATCTGATAG]
GAAGTTTGGATCTAAACACAACCTTAGTTCCAAAGTTTTTTTTCCAAACTTCCAACTTTCCATCACATCAAACCTTTCATACACACACAACTTTTCTATC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.80%	34.60%	0.40%	29.88%	CTGTCATACACACACAACTTTTCAATTTT: 0.13%; CTATCAGATCAACTTGTCATACACACACAACTTTTCAATTTT: 0.13%
All Indica	2759	48.70%	2.40%	0.62%	47.88%	CTATCAGATCAACTTGTCATACACACACAACTTTTCAATTTT: 0.22%; CTGTCATACACACACAACTTTTCAATTTT: 0.18%
All Japonica	1512	0.90%	96.90%	0.07%	2.12%	NA
Aus	269	87.00%	0.40%	0.00%	12.27%	CTGTCATACACACACAACTTTTCAATTTT: 0.37%
Indica I	595	34.50%	0.50%	0.17%	64.71%	CTGTCATACACACACAACTTTTCAATTTT: 0.17%
Indica II	465	62.40%	4.70%	0.65%	32.26%	NA
Indica III	913	45.70%	2.00%	1.20%	50.93%	CTGTCATACACACACAACTTTTCAATTTT: 0.22%
Indica Intermediate	786	54.80%	3.10%	0.25%	40.84%	CTATCAGATCAACTTGTCATACACACACAACTTTTCAATTTT: 0.76%; CTGTCATACACACACAACTTTTCAATTTT: 0.25%
Temperate Japonica	767	0.10%	99.20%	0.00%	0.65%	NA
Tropical Japonica	504	1.80%	93.50%	0.00%	4.76%	NA
Japonica Intermediate	241	1.70%	96.70%	0.41%	1.24%	NA
VI/Aromatic	96	24.00%	58.30%	0.00%	17.71%	NA
Intermediate	90	36.70%	52.20%	1.11%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0112718109	C -> T	LOC_Os01g22600-LOC_Os01g22620	intergenic_region ; MODIFIER	silent_mutation	Average:74.144; most accessible tissue: Minghui63 panicle, score: 87.605	N	N	N	N
vg0112718109	C -> CTGTCATACACACACAACTTTTCAATTTT	LOC_Os01g22600-LOC_Os01g22620	intergenic_region ; MODIFIER	silent_mutation	Average:74.144; most accessible tissue: Minghui63 panicle, score: 87.605	N	N	N	N
vg0112718109	C -> CTATCAGATCAACTTGTCATACACACACAA CTTTTCAATTTT	LOC_Os01g22600-LOC_Os01g22620	intergenic_region ; MODIFIER	silent_mutation	Average:74.144; most accessible tissue: Minghui63 panicle, score: 87.605	N	N	N	N
vg0112718109	C -> DEL	N	N	silent_mutation	Average:74.144; most accessible tissue: Minghui63 panicle, score: 87.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112718109	NA	2.68E-16	mr1146	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
vg0112718109	NA	6.05E-08	mr1222	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
vg0112718109	NA	2.32E-15	mr1040_2	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
vg0112718109	NA	2.02E-15	mr1162_2	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
vg0112718109	NA	6.20E-06	mr1543_2	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
vg0112718109	NA	6.54E-16	mr1836_2	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