Warnings for sample01-mixed-plasmids

Sample status

This table gives the status of each sample, either completed successfully or the reason the assembly failed. If applicable the mean quality for the whole construct has been provided, derived by Medaka from aligning the reads to the consensus.

The assembly was generated using Flye.
Sample Assembly completed / failed reason Length (bp) Mean Quality
sample01-mixed-plasmids Completed with warnings 3096 49.86
sample02-single-isolate Completed successfully 3036 48.96
sample03-single-isolate Completed successfully 3096 47.15

Plasmid Annotation

The Plasmid annotation plot and feature table are produced using pLannotate

A pLannotate plot is shown for each assembly. A feature table provides descriptions of the annotated sequence. Unfilled features on the plannotate plots are incomplete features; the sequence match in the plasmid covers less than 95% of the full length of the feature in the database. These elements may be leftover fragments from earlier cloning steps used to create a plasmid. If they include only a small fraction of the feature, they likely do not still have the annotated function. However, even small feature fragments may affect plasmid function if they result in cryptic gene expression or are inadvertently combined with other elements during later cloning steps. The plannotate plot may have overlapping annotation labels, use the zoom and hover tools to decipher the labels.

Feature Database Identity Match Length Description Start Location End Location Length (bp) Strand
TXL_EISFE swissprot 100.0% 100.0% Experimental evidence at protein level: Swiss-Prot protein existence level 1. Pore-forming toxin that defensively acts against parasitic microorganisms by forming pores in sphingomyelin-containing membranes. Has hemolytic activity and is also cytotoxic to spermatozoa of some species of invertebrates and many species of vertebrates and to amphibian larvae, guinea pig polymorphonuclear leukocytes, chicken fibroblasts, normal spleen cells and various tumor cells. Is lethal for various species of reptiles, amphibian, birds and mammals. Induces smooth muscle contraction. It binds sphingomyelin and induces hemolysis in the same manner as lysenin-related protein 2, and is 10-fold more effective than lysenin-related protein 1. 2501 296 891 +
rhaB promoter snapgene 100.0% 100.0% promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006) 2319 2438 119 +
cat promoter snapgene 100.0% 100.0% promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase 2132 2223 91 -
KanR snapgene 99.4% 100.0% aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes 1316 2132 816 -
CloDF13 ori snapgene 100.0% 92.3% Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins. 507 1189 682 -
T7 terminator snapgene 100.0% 100.0% transcription terminator for bacteriophage T7 RNA polymerase 326 374 48 +
kanMX snapgene 99.2% 57.9% yeast selectable marker conferring kanamycin resistance (Wach et al., 1994) 1316 2102 786 -
tonB terminator snapgene 100.0% 100.0% bidirectional E. coli tonB-P14 transcription terminator 2223 2255 32 -
T3Te terminator snapgene 100.0% 100.0% phage T3 early transcription terminator 471 501 30 +
RNAI Rfam 100.0% 99.0% Accession: RF00106 - RNAI 1086 1189 103 +
CloDF13 ori snapgene 99.0% 13.3% Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins. 1213 1310 98 -
PDK intron snapgene 100.0% 5.1% pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0 2131 2213 82 -
Feature Database Identity Match Length Description Start Location End Location Length (bp) Strand
csgG swissprot 100.0% 100.0% CSGG_ECO57 - Experimental evidence at protein level: Swiss-Prot protein existence level 1. May be involved in the biogenesis of curli organelles. From Escherichia coli O157:H7. 1621 2452 831 +
rhaB promoter snapgene 100.0% 100.0% promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006) 1439 1558 119 +
cat promoter snapgene 100.0% 100.0% promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase 1252 1343 91 -
KanR snapgene 99.4% 100.0% aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes 436 1252 816 -
CloDF13 ori snapgene 100.0% 92.3% Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins. 2663 309 682 -
T7 terminator snapgene 100.0% 100.0% transcription terminator for bacteriophage T7 RNA polymerase 2482 2530 48 +
kanMX snapgene 99.2% 57.9% yeast selectable marker conferring kanamycin resistance (Wach et al., 1994) 436 1222 786 -
tonB terminator snapgene 100.0% 100.0% bidirectional E. coli tonB-P14 transcription terminator 1343 1375 32 -
T3Te terminator snapgene 100.0% 100.0% phage T3 early transcription terminator 2627 2657 30 +
RNAI Rfam 100.0% 99.0% Accession: RF00106 - RNAI 206 309 103 +
CloDF13 ori snapgene 99.0% 13.3% Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins. 333 430 98 -
PDK intron snapgene 100.0% 5.1% pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0 1251 1333 82 -
Feature Database Identity Match Length Description Start Location End Location Length (bp) Strand
TXL_EISFE swissprot 100.0% 100.0% Experimental evidence at protein level: Swiss-Prot protein existence level 1. Pore-forming toxin that defensively acts against parasitic microorganisms by forming pores in sphingomyelin-containing membranes. Has hemolytic activity and is also cytotoxic to spermatozoa of some species of invertebrates and many species of vertebrates and to amphibian larvae, guinea pig polymorphonuclear leukocytes, chicken fibroblasts, normal spleen cells and various tumor cells. Is lethal for various species of reptiles, amphibian, birds and mammals. Induces smooth muscle contraction. It binds sphingomyelin and induces hemolysis in the same manner as lysenin-related protein 2, and is 10-fold more effective than lysenin-related protein 1. 2595 390 891 -
rhaB promoter snapgene 100.0% 100.0% promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006) 453 572 119 -
cat promoter snapgene 100.0% 100.0% promoter of the E. coli cat gene encoding chloramphenicol acetyltransferase 668 759 91 +
KanR snapgene 99.4% 100.0% aminoglycoside phosphotransferase; aph(3')-Ia; confers resistance to kanamycin in bacteria or G418 (Geneticin®) in eukaryotes 759 1575 816 +
CloDF13 ori snapgene 100.0% 92.3% Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins. 1702 2384 682 +
T7 terminator snapgene 100.0% 100.0% transcription terminator for bacteriophage T7 RNA polymerase 2517 2565 48 -
kanMX snapgene 99.2% 57.9% yeast selectable marker conferring kanamycin resistance (Wach et al., 1994) 789 1575 786 +
tonB terminator snapgene 100.0% 100.0% bidirectional E. coli tonB-P14 transcription terminator 636 668 32 +
T3Te terminator snapgene 100.0% 100.0% phage T3 early transcription terminator 2390 2420 30 -
RNAI Rfam 100.0% 99.0% Accession: RF00106 - RNAI 1700 1803 103 -
CloDF13 ori snapgene 99.0% 13.3% Plasmids containing the CloDF13 (CDF) origin of replication can be propagated in E. coli cells that contain additional plasmids with compatible origins. 1581 1678 98 +
PDK intron snapgene 100.0% 5.1% pdk; modified pyruvate orthophosphate dikinase intron from Flaveria trinervia 3.0 678 760 82 +

Read Counts

Number of reads per sample.

Read stats

For each assembly, read length statistics and plots of quality before and after host filtering, and after downsampling if a host reference was provided.

Completed successfully

Read count

5,336

Read count

197

Completed successfully

Read count

1,334

Read count

198

Completed successfully

Read count

1,334

Read count

197

Dot plots

These dot plots have been created by aligning the assembly to itself to reveal any repeats or repetitive regions. Black is for repeats found in the forward strand and red for repeats found in the reverse complement. Long unexpected repeat regions may indicate incorrect assembly, multiple insertions, recombination events, or other potential issues. Double-check that the repeated sequence is an intentional element of your plasmid. This was done using last

Software versions

Name Version
medaka 2.0.0
flye 2.9.4-b1799
minimap2 2.28-r1209
samtools 1.19.2
seqkit v2.4.0
Trycycler v0.5.5
bedtools v2.31.0
fastcat 0.18.6
rasusa 0.7.1
spoa 0.0.10
pandas 1.3.5
plannotate 1.2.0
bokeh 3.1.1

Workflow parameters

Key Value
out_dir /staging/plasmid-testing-v2-multi/work/wf-clone-validation
fastq /staging/plasmid-testing-v2-multi/fastqs
sample_sheet /staging/plasmid-testing-v2-multi/sample_sheet.csv
threads 32
bam None
db_directory None
host_reference None
regions_bedfile None
approx_size 7000
assm_coverage 60
trim_length 0
min_quality 9
prefix None
primers None
insert_reference None
sample None
analyse_unclassified False
override_basecaller_cfg None
medaka_model_path None
flye_quality nano-hq
non_uniform_coverage False
large_construct False
full_reference None
cutsite_mismatch 1
primer_mismatch 2
expected_coverage 95
expected_identity 99
assembly_tool flye
canu_fast False
client_fields None
store_dir None