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SourceForge net samtools mpileup
Samtools Mpileup, supplied by SourceForge net, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/samtools+mpileup/samtools+mpileup/pm39800378-71-9-12
Average 90 stars, based on 1 article reviews
samtools mpileup - by Bioz Stars, 2026-11
90/100 stars

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Related Articles

Sequencing:

Article Title: Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes
Article Snippet: After alignment to the reference genome, all genomic samples were analyzed with samtools (version 0.1.18) mpileup ( http://samtools.sourceforge.net ) to calculate read coverage depth across the genome.

Article Title: A rare codon-based translational program of cell proliferation
Article Snippet: Thus, the level of A34I modifications was quantified by measuring the A-to-G substitutions at the anticodon wobble position using samtools mpileup v1.9 ( http://samtools.sourceforge.ne t) [ ] and VarScan v2.4.1 ( http://varscan.sourceforge.net ) [ ]: samtools mpileup -B -f reference.fa sample.sam | java -jar VarScan.v2.4.1.jar mpileup2snp --min-coverage 10 --min-var-freq 0 --p-value 0.05 --variants --output-vcf --strand-filter 0

Article Title: Discovery of Genome-Wide DNA Polymorphisms and Resistance-Relative Genes in Chaling Wild Rice (Oryza rufipogon Griff.) by Whole-Genome Sequencing
Article Snippet: Chaling common wild rice (Chaling CWR, Oryza rufipogon Griff.) is a kind of germplasm resource which possesses abundant genetic diversity and plays a pivotal role in improving cultivated rice.. In this research, we used next-generation sequencing technology to reveal the genome sequence of Chaling CWR and investigate its elite genes.. The results showed that the average coverage was 93.99%.

Mass Spectrometry:

Article Title: Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes
Article Snippet: After alignment to the reference genome, all genomic samples were analyzed with samtools (version 0.1.18) mpileup ( http://samtools.sourceforge.net ) to calculate read coverage depth across the genome.

Article Title: A rare codon-based translational program of cell proliferation
Article Snippet: Thus, the level of A34I modifications was quantified by measuring the A-to-G substitutions at the anticodon wobble position using samtools mpileup v1.9 ( http://samtools.sourceforge.ne t) [ ] and VarScan v2.4.1 ( http://varscan.sourceforge.net ) [ ]: samtools mpileup -B -f reference.fa sample.sam | java -jar VarScan.v2.4.1.jar mpileup2snp --min-coverage 10 --min-var-freq 0 --p-value 0.05 --variants --output-vcf --strand-filter 0

Article Title: Discovery of Genome-Wide DNA Polymorphisms and Resistance-Relative Genes in Chaling Wild Rice (Oryza rufipogon Griff.) by Whole-Genome Sequencing
Article Snippet: Chaling common wild rice (Chaling CWR, Oryza rufipogon Griff.) is a kind of germplasm resource which possesses abundant genetic diversity and plays a pivotal role in improving cultivated rice.. In this research, we used next-generation sequencing technology to reveal the genome sequence of Chaling CWR and investigate its elite genes.. The results showed that the average coverage was 93.99%.

Metaproteomics:

Article Title: Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes
Article Snippet: After alignment to the reference genome, all genomic samples were analyzed with samtools (version 0.1.18) mpileup ( http://samtools.sourceforge.net ) to calculate read coverage depth across the genome.

Article Title: A rare codon-based translational program of cell proliferation
Article Snippet: Thus, the level of A34I modifications was quantified by measuring the A-to-G substitutions at the anticodon wobble position using samtools mpileup v1.9 ( http://samtools.sourceforge.ne t) [ ] and VarScan v2.4.1 ( http://varscan.sourceforge.net ) [ ]: samtools mpileup -B -f reference.fa sample.sam | java -jar VarScan.v2.4.1.jar mpileup2snp --min-coverage 10 --min-var-freq 0 --p-value 0.05 --variants --output-vcf --strand-filter 0

Article Title: Discovery of Genome-Wide DNA Polymorphisms and Resistance-Relative Genes in Chaling Wild Rice (Oryza rufipogon Griff.) by Whole-Genome Sequencing
Article Snippet: Chaling common wild rice (Chaling CWR, Oryza rufipogon Griff.) is a kind of germplasm resource which possesses abundant genetic diversity and plays a pivotal role in improving cultivated rice.. In this research, we used next-generation sequencing technology to reveal the genome sequence of Chaling CWR and investigate its elite genes.. The results showed that the average coverage was 93.99%.

Software:

Article Title: Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes
Article Snippet: After alignment to the reference genome, all genomic samples were analyzed with samtools (version 0.1.18) mpileup ( http://samtools.sourceforge.net ) to calculate read coverage depth across the genome.

Article Title: A rare codon-based translational program of cell proliferation
Article Snippet: Thus, the level of A34I modifications was quantified by measuring the A-to-G substitutions at the anticodon wobble position using samtools mpileup v1.9 ( http://samtools.sourceforge.ne t) [ ] and VarScan v2.4.1 ( http://varscan.sourceforge.net ) [ ]: samtools mpileup -B -f reference.fa sample.sam | java -jar VarScan.v2.4.1.jar mpileup2snp --min-coverage 10 --min-var-freq 0 --p-value 0.05 --variants --output-vcf --strand-filter 0

Article Title: Discovery of Genome-Wide DNA Polymorphisms and Resistance-Relative Genes in Chaling Wild Rice (Oryza rufipogon Griff.) by Whole-Genome Sequencing
Article Snippet: Chaling common wild rice (Chaling CWR, Oryza rufipogon Griff.) is a kind of germplasm resource which possesses abundant genetic diversity and plays a pivotal role in improving cultivated rice.. In this research, we used next-generation sequencing technology to reveal the genome sequence of Chaling CWR and investigate its elite genes.. The results showed that the average coverage was 93.99%.

Variant Assay:

Article Title: Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes
Article Snippet: After alignment to the reference genome, all genomic samples were analyzed with samtools (version 0.1.18) mpileup ( http://samtools.sourceforge.net ) to calculate read coverage depth across the genome.

Article Title: A rare codon-based translational program of cell proliferation
Article Snippet: Thus, the level of A34I modifications was quantified by measuring the A-to-G substitutions at the anticodon wobble position using samtools mpileup v1.9 ( http://samtools.sourceforge.ne t) [ ] and VarScan v2.4.1 ( http://varscan.sourceforge.net ) [ ]: samtools mpileup -B -f reference.fa sample.sam | java -jar VarScan.v2.4.1.jar mpileup2snp --min-coverage 10 --min-var-freq 0 --p-value 0.05 --variants --output-vcf --strand-filter 0

Article Title: Discovery of Genome-Wide DNA Polymorphisms and Resistance-Relative Genes in Chaling Wild Rice (Oryza rufipogon Griff.) by Whole-Genome Sequencing
Article Snippet: Chaling common wild rice (Chaling CWR, Oryza rufipogon Griff.) is a kind of germplasm resource which possesses abundant genetic diversity and plays a pivotal role in improving cultivated rice.. In this research, we used next-generation sequencing technology to reveal the genome sequence of Chaling CWR and investigate its elite genes.. The results showed that the average coverage was 93.99%.

Next-Generation Sequencing:

Article Title: Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes
Article Snippet: After alignment to the reference genome, all genomic samples were analyzed with samtools (version 0.1.18) mpileup ( http://samtools.sourceforge.net ) to calculate read coverage depth across the genome.

Article Title: A rare codon-based translational program of cell proliferation
Article Snippet: Thus, the level of A34I modifications was quantified by measuring the A-to-G substitutions at the anticodon wobble position using samtools mpileup v1.9 ( http://samtools.sourceforge.ne t) [ ] and VarScan v2.4.1 ( http://varscan.sourceforge.net ) [ ]: samtools mpileup -B -f reference.fa sample.sam | java -jar VarScan.v2.4.1.jar mpileup2snp --min-coverage 10 --min-var-freq 0 --p-value 0.05 --variants --output-vcf --strand-filter 0

Article Title: Discovery of Genome-Wide DNA Polymorphisms and Resistance-Relative Genes in Chaling Wild Rice (Oryza rufipogon Griff.) by Whole-Genome Sequencing
Article Snippet: Chaling common wild rice (Chaling CWR, Oryza rufipogon Griff.) is a kind of germplasm resource which possesses abundant genetic diversity and plays a pivotal role in improving cultivated rice.. In this research, we used next-generation sequencing technology to reveal the genome sequence of Chaling CWR and investigate its elite genes.. The results showed that the average coverage was 93.99%.

Bacteria:

Article Title: Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes
Article Snippet: After alignment to the reference genome, all genomic samples were analyzed with samtools (version 0.1.18) mpileup ( http://samtools.sourceforge.net ) to calculate read coverage depth across the genome.

Article Title: A rare codon-based translational program of cell proliferation
Article Snippet: Thus, the level of A34I modifications was quantified by measuring the A-to-G substitutions at the anticodon wobble position using samtools mpileup v1.9 ( http://samtools.sourceforge.ne t) [ ] and VarScan v2.4.1 ( http://varscan.sourceforge.net ) [ ]: samtools mpileup -B -f reference.fa sample.sam | java -jar VarScan.v2.4.1.jar mpileup2snp --min-coverage 10 --min-var-freq 0 --p-value 0.05 --variants --output-vcf --strand-filter 0

Article Title: Discovery of Genome-Wide DNA Polymorphisms and Resistance-Relative Genes in Chaling Wild Rice (Oryza rufipogon Griff.) by Whole-Genome Sequencing
Article Snippet: Chaling common wild rice (Chaling CWR, Oryza rufipogon Griff.) is a kind of germplasm resource which possesses abundant genetic diversity and plays a pivotal role in improving cultivated rice.. In this research, we used next-generation sequencing technology to reveal the genome sequence of Chaling CWR and investigate its elite genes.. The results showed that the average coverage was 93.99%.

Mutagenesis:

Article Title: Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes
Article Snippet: After alignment to the reference genome, all genomic samples were analyzed with samtools (version 0.1.18) mpileup ( http://samtools.sourceforge.net ) to calculate read coverage depth across the genome.

Article Title: A rare codon-based translational program of cell proliferation
Article Snippet: Thus, the level of A34I modifications was quantified by measuring the A-to-G substitutions at the anticodon wobble position using samtools mpileup v1.9 ( http://samtools.sourceforge.ne t) [ ] and VarScan v2.4.1 ( http://varscan.sourceforge.net ) [ ]: samtools mpileup -B -f reference.fa sample.sam | java -jar VarScan.v2.4.1.jar mpileup2snp --min-coverage 10 --min-var-freq 0 --p-value 0.05 --variants --output-vcf --strand-filter 0

Article Title: Discovery of Genome-Wide DNA Polymorphisms and Resistance-Relative Genes in Chaling Wild Rice (Oryza rufipogon Griff.) by Whole-Genome Sequencing
Article Snippet: Chaling common wild rice (Chaling CWR, Oryza rufipogon Griff.) is a kind of germplasm resource which possesses abundant genetic diversity and plays a pivotal role in improving cultivated rice.. In this research, we used next-generation sequencing technology to reveal the genome sequence of Chaling CWR and investigate its elite genes.. The results showed that the average coverage was 93.99%.



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