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Detailed information for vg0609181739:

Variant ID: vg0609181739 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9181739
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGGGTGAGTTTGATGAGGTTGAGTATATAGGAGTTAGTGATGAGAGGGAGAATTACAATGAGCTGGTGTCAGATGATGAGGCTAATGATCCAGATTACA[C/T]
TCCTGAGGATGATGATGCTGATGAAGAGAATGATGATCCTAAGGTGTATGAGACAATATGTTGTCCTGAAAGAGGTTGAACTTGCAGTTCCCTACTCTGA

Reverse complement sequence

TCAGAGTAGGGAACTGCAAGTTCAACCTCTTTCAGGACAACATATTGTCTCATACACCTTAGGATCATCATTCTCTTCATCAGCATCATCATCCTCAGGA[G/A]
TGTAATCTGGATCATTAGCCTCATCATCTGACACCAGCTCATTGTAATTCTCCCTCTCATCACTAACTCCTATATACTCAACCTCATCAAACTCACCCCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.90%	2.70%	2.09%	39.25%	NA
All Indica	2759	70.80%	4.60%	2.72%	21.93%	NA
All Japonica	1512	41.50%	0.10%	1.12%	57.28%	NA
Aus	269	3.30%	0.00%	1.49%	95.17%	NA
Indica I	595	76.30%	10.90%	5.38%	7.39%	NA
Indica II	465	83.40%	0.00%	1.29%	15.27%	NA
Indica III	913	64.40%	2.40%	0.88%	32.31%	NA
Indica Intermediate	786	66.40%	5.10%	3.69%	24.81%	NA
Temperate Japonica	767	74.40%	0.00%	1.43%	24.12%	NA
Tropical Japonica	504	4.40%	0.00%	0.40%	95.24%	NA
Japonica Intermediate	241	14.50%	0.40%	1.66%	83.40%	NA
VI/Aromatic	96	5.20%	0.00%	1.04%	93.75%	NA
Intermediate	90	54.40%	1.10%	2.22%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0609181739	C -> T	LOC_Os06g16130.1	missense_variant ; p.Thr185Ile; MODERATE	nonsynonymous_codon ; T185I	Average:45.1; most accessible tissue: Zhenshan97 young leaf, score: 60.8	unknown	unknown	TOLERATED	0.06
vg0609181739	C -> DEL	LOC_Os06g16130.1	N	frameshift_variant	Average:45.1; most accessible tissue: Zhenshan97 young leaf, score: 60.8	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609181739	5.50E-06	1.94E-08	mr1097	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