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Detailed information for vg0141497668:

Variant ID: vg0141497668 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 41497668
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACGTTCAGAGCGCATGAGGACTAGAGTTCACGGAACAGGTACCACTATTGTTAGTAACCTAATACTGGGCCATGACTAAGCTAATGATTATTGGCAAGT[T/C]
ATGGACTGCGGGTAAAGCGTACATCTACTGCAGTATGAATATTCTTAAAACTATTCGAATAGCCGTGCTCATGGACTTGAGTATCGGGACTCATATGGTA

Reverse complement sequence

TACCATATGAGTCCCGATACTCAAGTCCATGAGCACGGCTATTCGAATAGTTTTAAGAATATTCATACTGCAGTAGATGTACGCTTTACCCGCAGTCCAT[A/G]
ACTTGCCAATAATCATTAGCTTAGTCATGGCCCAGTATTAGGTTACTAACAATAGTGGTACCTGTTCCGTGAACTCTAGTCCTCATGCGCTCTGAACGTA

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	63.10%	3.70%	4.82%	28.40%	NA
All Indica	2759	42.50%	5.50%	7.36%	44.65%	NA
All Japonica	1512	98.70%	0.00%	0.13%	1.19%	NA
Aus	269	55.80%	7.40%	8.18%	28.62%	NA
Indica I	595	81.50%	1.80%	1.68%	14.96%	NA
Indica II	465	20.20%	7.30%	9.25%	63.23%	NA
Indica III	913	26.10%	7.70%	9.64%	56.63%	NA
Indica Intermediate	786	45.20%	4.70%	7.89%	42.24%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	97.00%	0.00%	0.40%	2.58%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	NA
Intermediate	90	82.20%	3.30%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0141497668	T -> DEL	N	N	silent_mutation	Average:8.582; most accessible tissue: Callus, score: 18.986	N	N	N	N
vg0141497668	T -> C	LOC_Os01g71620.1	upstream_gene_variant ; 3222.0bp to feature; MODIFIER	silent_mutation	Average:8.582; most accessible tissue: Callus, score: 18.986	N	N	N	N
vg0141497668	T -> C	LOC_Os01g71624.1	intron_variant ; MODIFIER	silent_mutation	Average:8.582; most accessible tissue: Callus, score: 18.986	N	N	N	N
vg0141497668	T -> C	LOC_Os01g71624.4	intron_variant ; MODIFIER	silent_mutation	Average:8.582; most accessible tissue: Callus, score: 18.986	N	N	N	N
vg0141497668	T -> C	LOC_Os01g71624.3	intron_variant ; MODIFIER	silent_mutation	Average:8.582; most accessible tissue: Callus, score: 18.986	N	N	N	N
vg0141497668	T -> C	LOC_Os01g71624.2	intron_variant ; MODIFIER	silent_mutation	Average:8.582; most accessible tissue: Callus, score: 18.986	N	N	N	N
vg0141497668	T -> C	LOC_Os01g71624.5	intron_variant ; MODIFIER	silent_mutation	Average:8.582; most accessible tissue: Callus, score: 18.986	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0141497668	4.62E-06	NA	mr1089_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