Read depth of mitochondrial contigs
WebMay 22, 2024 · The final assembly of O. subterraneum has an average read depth of ~ 71×, ranging between 40 × and 113 × across the 54 mitochondrial chromosomes (Supporting Information Table S2). The genome shows a continuous and relatively even read depth with no gaps or low-coverage regions (Supporting Information Figure S1). WebAug 28, 2015 · Mitochondrial disease is one of the most common groups of genetic diseases with a minimum prevalence of greater than 1 in 5000 in adults. Whilst multi …
Read depth of mitochondrial contigs
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WebDec 9, 2024 · All assembled contigs were blasted to the Marchantia polymorpha mt genome (GenBank accession: NC_001660) to identify mt contigs. As the genomes of the three cellular compartments are significantly different in copy numbers and hence read coverage in sequencing [ 44 ], the read depth for mt contigs is distinctly lower than that of plastid ... WebApr 10, 2024 · This study identified a spectrum of nuclear and mitochondrial genome mutations in early-stage lung adenocarcinoma and explored their association with diagnosis. ... plasma cfDNA samples from LUAD were subjected to targeted sequencing using a custom 115 gene panel to a median unique read depth of ×368. This research …
WebJun 8, 2024 · Single-copy contigs will have a median depth dx close to D, the median depth per base across the entire assembly, while repeat contigs will have a median depth near a … WebJul 24, 2024 · Mitochondrial contigs were identified in each draft assembly by BLASTn program (Chen et al. 2015) using the mitochondrial genome sequences of eight related Lamiales species (Table S1) as query sequences. Based on the average depth and the number of matched hits, a self-looping contig numbered utg602 was selected as the …
Web... contig N50 value was 386 bp, and the longest length was 42,272 bp. There were some contigs with length > 5 kb and high read depth, which were separated with other, shorter …
WebThe outcome of an assembly is a set of contigs. A contig is a con-tiguous assembled piece of DNA sequence. Some assemblers also compute scaffolds, which is a set of contigs for …
WebNational Center for Biotechnology Information real ales onlineWebMar 29, 2024 · contigs = get_contigs ( bam) # Guess mitochondrial chromosome mtchr = [ x for x in contigs if x. lower (). find ( "m") == 0] if len ( mtchr) != 1: mtchr = None else: mtchr = mtchr [ 0] coverage_dict = {} for c in contigs. keys (): command = "samtools depth -r %s %s awk ' {sum+=$3;cnt++}END {print cnt \"\t\" sum}'" % ( c, bam) real ale pubs waterlooWebAug 1, 2024 · including sequencing depth, read lengths, contig sizes, GC-content, assembly sizes, N50 values or number of gaps. Optionally, if a reference genome and an annotation file (GFF format) ar e provided, real ale wobbleWebJan 10, 2024 · In this paper, we used read depth contigs over 100× as chloroplast genome candidate contigs and contigs between 50× and 100× as mitochondrial genome … real ale way westerhamWebSep 20, 2014 · To use the script, feed the function coverage a bam file, and the function will return a dictionary of the depth of coverage, breadth of coverage, sum of depths (at every position), and number of bases mapped, for every contig/chromosome individually, and the entire genome as a whole. how to tame a beast hogwarts legacyWebThe default value is 1,000 bp which may be too high for mitochondrial contigs assembled from off-target reads. The same applies for the parameter --blast-size (default: 30%). Trimmed single-end reads mitofinder -j [seqid] -s [SE_reads.fastq.gz] -r [genbank_reference.gb] -o [genetic_code] -p [threads] -m [memory] real ale trail wrexhamWebNext, BlastN was applied to extract the potential mitochondrial contigs using other three Populus mitogenomes (P. alba, P. davidiana, and P. tremula) as references (Altschul et al., 1990), and all potential mitochondrial contigs were then confirmed based on their read depths (Supplementary Figure S1). how to tame a boar in minecraft