arrow_drop_down
readhit
dark_mode
account_circle
home
read
hit
Align reads to one short reference and see coverage, differences and the consensus.
upload_file
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.
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.
New here? See what readhit can do →