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Detailed information for vg1006141936:

Variant ID: vg1006141936 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 6141936
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTCTCCGGAAACTCCGAATCTATCGAAAAGAAGCAATGTGCGAATAAGAGCCAAATAAACATGCACATGCAAAATGATCAATAAATTATGAAATAAATA[T/C]
AGTGGGTAGAGCACATGTTAACTTGAATTTAGGTGAAAGAATCACTAGATTATCACTTATAGTTTGGGAGATATGAAAATGACAAGCTTTCAGGTGCTGA

Reverse complement sequence

TCAGCACCTGAAAGCTTGTCATTTTCATATCTCCCAAACTATAAGTGATAATCTAGTGATTCTTTCACCTAAATTCAAGTTAACATGTGCTCTACCCACT[A/G]
TATTTATTTCATAATTTATTGATCATTTTGCATGTGCATGTTTATTTGGCTCTTATTCGCACATTGCTTCTTTTCGATAGATTCGGAGTTTCCGGAGAGT

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	62.70%	18.90%	1.69%	16.74%	NA
All Indica	2759	77.80%	1.20%	1.01%	19.93%	NA
All Japonica	1512	26.40%	54.90%	3.37%	15.34%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	98.30%	0.20%	0.00%	1.51%	NA
Indica II	465	78.70%	1.30%	1.51%	18.49%	NA
Indica III	913	62.90%	2.00%	0.99%	34.17%	NA
Indica Intermediate	786	79.10%	1.10%	1.53%	18.19%	NA
Temperate Japonica	767	28.80%	62.50%	4.95%	3.78%	NA
Tropical Japonica	504	26.00%	44.80%	0.79%	28.37%	NA
Japonica Intermediate	241	19.50%	51.90%	3.73%	24.90%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	58.90%	30.00%	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
vg1006141936	T -> C	LOC_Os10g11110.1	upstream_gene_variant ; 2653.0bp to feature; MODIFIER	silent_mutation	Average:19.464; most accessible tissue: Callus, score: 72.134	N	N	N	N
vg1006141936	T -> C	LOC_Os10g11100.1	intron_variant ; MODIFIER	silent_mutation	Average:19.464; most accessible tissue: Callus, score: 72.134	N	N	N	N
vg1006141936	T -> DEL	N	N	silent_mutation	Average:19.464; most accessible tissue: Callus, score: 72.134	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1006141936	4.33E-06	NA	mr1922	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