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Align reads to one short reference and see coverage, differences and the consensus.
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Drop the reference
drag it here or click to browse — FASTA, GenBank, .ab1 · reads come next
Or paste a sequence
Use this sequence
or open a ready-made set
Plasmid, three Sanger traces
Three .ab1 reads of a 4.7 kb CRISPR construct against its deposited map. The reads agree with each other to 99%, and disagree with the map in exactly two places — the 20 bp gRNA spacers behind each U6 promoter, one of which this clone carries differently. Clone checking, as it actually goes.
Amplicon, 400 Illumina reads
A 450 bp window of the SARS-CoV-2 spike at 400× depth, from both ends of one ARTIC amplicon. Every read carries the same 3 bp deletion — ΔY144, the NTD deletion of lineage Alpha. COG-UK data.
Already mapped: 150 long reads
A 1.6 kb window of the spike, covered by 150 PacBio HiFi reads of about 720 bp each — opened as minimap2 left them, a position and a CIGAR per read, so nothing is aligned here at all. A row crosses half the target instead of a fifteenth of it, which is what a long-read pileup looks like. This Delta specimen carries T95I, G142D, a 6 bp deletion at Δ156–157, L452R and T478K, every one of them spelled out in the CIGARs rather than found.
Nanopore, 120 reads
A 1.1 kb spike window at about 95% identity — an Omicron BA.5 specimen whose thirteen RBD substitutions are somewhere in there. Every read carries its own insertions, which would otherwise turn the target’s 1111 columns into about 2000 of mostly one base and a gap; folded by default, the minority ones collapse back into a mark and the alignment reads like any other.
One specimen, both methods
A 580 bp window of ORF6/ORF7a with two Sanger reads and 250 Illumina reads of the SAME specimen — Sanger over a pileup, which is why this is one tool and not two.
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