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Detailed information for vg0626891249:

Variant ID: vg0626891249 (JBrowse)	Variation Type: INDEL
Chromosome: chr06	Position: 26891249
Reference Allele: T	Alternative Allele: C,TAA
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

ATGATGGTGCAGTCCCTCTAACCCCCGATGAAAACTAAGTCACTAATGTTAAGGGGGCGGCTAGCCAATATCATTGGCGCCGAGGACCAATTTGTTTTTT[T/C,TAA]
TAAAAAAATAACCTATTTGTAGCAGAAAAGAGTCCATTTGTAATTAAAAAAGGGAGTAGCTATATTTATGGCGCCATATTTTTCACCAAAAAATAGTCAG

Reverse complement sequence

CTGACTATTTTTTGGTGAAAAATATGGCGCCATAAATATAGCTACTCCCTTTTTTAATTACAAATGGACTCTTTTCTGCTACAAATAGGTTATTTTTTTA[A/G,TTA]
AAAAAACAAATTGGTCCTCGGCGCCAATGATATTGGCTAGCCGCCCCCTTAACATTAGTGACTTAGTTTTCATCGGGGGTTAGAGGGACTGCACCATCAT

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	91.20%	8.30%	0.47%	0.00%	TAA: 0.04%
All Indica	2759	98.10%	1.80%	0.11%	0.00%	NA
All Japonica	1512	77.30%	21.60%	1.12%	0.00%	NA
Aus	269	97.00%	1.50%	0.74%	0.00%	TAA: 0.74%
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	95.90%	3.70%	0.43%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	95.90%	3.90%	0.13%	0.00%	NA
Temperate Japonica	767	95.20%	3.30%	1.56%	0.00%	NA
Tropical Japonica	504	43.70%	55.60%	0.79%	0.00%	NA
Japonica Intermediate	241	90.90%	8.70%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0626891249	T -> C	LOC_Os06g44530.1	intron_variant ; MODIFIER	silent_mutation	Average:62.826; most accessible tissue: Minghui63 flower, score: 83.608	N	N	N	N
vg0626891249	T -> TAA	LOC_Os06g44530.1	intron_variant ; MODIFIER	silent_mutation	Average:62.826; most accessible tissue: Minghui63 flower, score: 83.608	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0626891249	5.58E-06	NA	mr1107	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
vg0626891249	NA	1.04E-06	mr1039_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
vg0626891249	6.85E-09	NA	mr1082_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
vg0626891249	NA	8.11E-06	mr1082_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
vg0626891249	1.74E-07	NA	mr1083_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
vg0626891249	8.10E-07	NA	mr1104_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
vg0626891249	5.74E-07	NA	mr1107_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
vg0626891249	3.41E-06	NA	mr1145_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
vg0626891249	8.12E-06	NA	mr1226_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
vg0626891249	3.21E-06	NA	mr1264_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
vg0626891249	NA	1.39E-10	mr1408_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
vg0626891249	NA	3.64E-14	mr1410_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
vg0626891249	NA	1.79E-06	mr1632_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
vg0626891249	NA	7.21E-10	mr1696_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
vg0626891249	NA	2.27E-06	mr1860_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