Sample summary

Barcode Alias Read count Median read length Contig count MLST Species call (ANI | Fraction query)
barcode01 barcode01 1715 3507.0 1 - Listeria monocytogenes_B (- | 0.500)
barcode02 barcode02 1229 3504.0 1 - -
MLST: Multi-locus sequence typing
ANI: Average Nucleotide Identity
Fraction query: Fraction of query genome matched to reference

Read summary

Reads were filtered and summary statistics were generated using fastcat.
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Variant calling

The following tables and figures are derived from the output of bcftools stats.



Variant counts:
sample MNPs SNPs indels multiallelic SNP sites multiallelic sites no-ALTs others records
barcode01 1 287 580 0 0 0 196 1064
barcode02 1 285 582 0 0 0 195 1063

Transitions and transversions:
sample ts tv ts/tv ts (1st ALT) tv (1st ALT) ts/tv (1st ALT)
barcode01 84 203 0.41 84 203 0.41
barcode02 83 202 0.41 83 202 0.41

Base substitution types and indel lengths:

Base substitutions were symmetrised by pairing.
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Plasmid identification

Plasmid identification was performed using MOB-suite
Use the dropdown menu to view different samples.
Click on each plasmid cluster to view detailed information about the contigs.

MOB-suite did not identify plasmid contigs in this assembly.
MOB-suite did not identify plasmid contigs in this assembly.

Annotations

The contigs were annotated with Bakta.
You can use the dropdown menu to view different samples.

Contig ID Start End Strand Gene Product EC_number
lmonocytogenes lmonocytogenes 1 61970 + - - -
lmonocytogenes FONMIA_001 117 578 + - hypothetical protein -
lmonocytogenes FONMIA_002 872 1093 + - hypothetical protein -
lmonocytogenes FONMIA_003 2474 2590 + - hypothetical protein -
lmonocytogenes FONMIA_004 2580 2843 + - hypothetical protein -
lmonocytogenes FONMIA_005 2952 3365 - - hypothetical protein -
lmonocytogenes FONMIA_006 7276 7506 - - hypothetical protein -
lmonocytogenes FONMIA_007 7605 7733 + - hypothetical protein -
lmonocytogenes FONMIA_008 10108 10431 - - hypothetical protein -
lmonocytogenes FONMIA_009 10444 10833 + - hypothetical protein -
lmonocytogenes FONMIA_010 11225 11590 - - hypothetical protein -
lmonocytogenes FONMIA_011 11706 12290 - - Putative Zn-dependent hydrolases putative hydroxyacylglutathione hydrolase -
lmonocytogenes FONMIA_012 12574 12843 - - hypothetical protein -
lmonocytogenes FONMIA_013 13510 13953 + - hypothetical protein -
lmonocytogenes FONMIA_014 14042 14401 + - hypothetical protein -
lmonocytogenes FONMIA_015 15113 15481 - - hypothetical protein -
lmonocytogenes FONMIA_016 15594 15890 - - hypothetical protein -
lmonocytogenes FONMIA_017 16016 17338 + rrs 16S ribosomal RNA -
lmonocytogenes FONMIA_018 17581 20302 + rrl 23S ribosomal RNA -
lmonocytogenes FONMIA_019 20524 20730 + - hypothetical protein -
lmonocytogenes FONMIA_020 21930 22070 + - hypothetical protein -
lmonocytogenes FONMIA_021 22531 22749 + - hypothetical protein -
lmonocytogenes FONMIA_022 22721 22957 - - hypothetical protein -
lmonocytogenes FONMIA_023 23522 23686 + - hypothetical protein -
lmonocytogenes FONMIA_024 23920 24342 - - hypothetical protein -
lmonocytogenes FONMIA_025 24810 25019 + - hypothetical protein -
lmonocytogenes FONMIA_026 25035 25526 + - hypothetical protein -
lmonocytogenes FONMIA_027 25604 26008 + - hypothetical protein -
lmonocytogenes FONMIA_028 26005 26376 + - hypothetical protein -
lmonocytogenes FONMIA_029 26395 26640 + - hypothetical protein -
lmonocytogenes FONMIA_030 27125 27454 + - hypothetical protein -
lmonocytogenes FONMIA_031 27700 27843 + - hypothetical protein -
lmonocytogenes FONMIA_032 27876 28046 + - hypothetical protein -
lmonocytogenes FONMIA_033 28085 28390 + - hypothetical protein -
lmonocytogenes FONMIA_034 28417 28719 + - hypothetical protein -
lmonocytogenes FONMIA_035 28885 29226 + - hypothetical protein -
lmonocytogenes FONMIA_036 29251 29757 + - hypothetical protein -
lmonocytogenes FONMIA_037 29851 30492 + - hypothetical protein -
lmonocytogenes FONMIA_038 30631 30795 + - hypothetical protein -
lmonocytogenes FONMIA_039 30785 30928 + - hypothetical protein -
lmonocytogenes FONMIA_040 30945 31166 + - hypothetical protein -
lmonocytogenes FONMIA_041 31261 31551 - - hypothetical protein -
lmonocytogenes FONMIA_042 32022 32159 - - hypothetical protein -
lmonocytogenes FONMIA_043 33008 33367 - - hypothetical protein -
lmonocytogenes FONMIA_044 33958 34143 - - hypothetical protein -
lmonocytogenes FONMIA_045 34692 34880 + - hypothetical protein -
lmonocytogenes FONMIA_046 35338 35514 - - hypothetical protein -
lmonocytogenes FONMIA_047 36542 36835 + - hypothetical protein -
lmonocytogenes FONMIA_048 37058 37708 + - hypothetical protein -
lmonocytogenes FONMIA_049 38776 38913 + - hypothetical protein -
lmonocytogenes FONMIA_050 38940 39200 + - hypothetical protein -
lmonocytogenes FONMIA_051 39518 40105 + - hypothetical protein -
lmonocytogenes FONMIA_052 40129 40401 + - hypothetical protein -
lmonocytogenes FONMIA_053 40359 40544 + - hypothetical protein -
lmonocytogenes FONMIA_054 40607 41125 + - hypothetical protein -
lmonocytogenes FONMIA_055 41562 42113 + - Molybdate metabolism regulator -
lmonocytogenes FONMIA_056 43319 44101 + virB ABC transporter ATP-binding protein VirB -
lmonocytogenes FONMIA_057 44091 44627 + - hypothetical protein -
lmonocytogenes FONMIA_058 44581 45825 + - hypothetical protein -
lmonocytogenes FONMIA_059 46132 46554 + - hypothetical protein -
lmonocytogenes FONMIA_060 46610 46810 + - hypothetical protein -
lmonocytogenes FONMIA_061 46880 47755 + - NAD-dependent epimerase/dehydratase domain-containing protein -
lmonocytogenes FONMIA_062 47775 48020 + - hypothetical protein -
lmonocytogenes FONMIA_063 48475 48777 - - hypothetical protein -
lmonocytogenes FONMIA_064 49476 50159 + - hypothetical protein -
lmonocytogenes FONMIA_065 50271 50519 + - hypothetical protein -
lmonocytogenes FONMIAIEMO_3 50619 50859 + - T-box leader -
lmonocytogenes FONMIA_066 50917 51420 + - hypothetical protein -
lmonocytogenes FONMIA_067 51438 51557 + - hypothetical protein -
lmonocytogenes FONMIA_068 51568 51840 + - hypothetical protein -
lmonocytogenes FONMIA_069 51962 52219 + - hypothetical protein -
lmonocytogenes FONMIA_070 52221 52592 + - hypothetical protein -
lmonocytogenes FONMIA_071 53912 54172 - - hypothetical protein -
lmonocytogenes FONMIA_072 55118 55603 - - hypothetical protein -
lmonocytogenes FONMIA_073 55554 55748 - - hypothetical protein -
lmonocytogenes FONMIA_074 56175 56417 - - hypothetical protein -
lmonocytogenes FONMIA_075 56740 57006 - - hypothetical protein -
lmonocytogenes FONMIA_076 57093 57404 - - hypothetical protein -
lmonocytogenes FONMIA_077 57590 57826 - - hypothetical protein -
lmonocytogenes FONMIA_078 57838 57948 - - hypothetical protein -
lmonocytogenes FONMIA_079 59403 59543 + - hypothetical protein -
lmonocytogenes FONMIA_080 60348 60608 + - hypothetical protein -
lmonocytogenes FONMIA_081 60861 61109 + - hypothetical protein -
lmonocytogenes FONMIA_082 61152 61337 + - hypothetical protein -
lmonocytogenes FONMIA_083 61309 61800 - - hypothetical protein -
Contig ID Start End Strand Gene Product EC_number
lmonocytogenes lmonocytogenes 1 60353 + - - -
lmonocytogenes MJKNJD_001 49 492 + - hypothetical protein -
lmonocytogenes MJKNJD_002 763 1242 + - hypothetical protein -
lmonocytogenes MJKNJD_003 1372 1620 - - hypothetical protein -
lmonocytogenes MJKNJD_004 2510 2743 + acpP Acyl carrier protein AcpP -
lmonocytogenes MJKNJD_005 2776 2874 + - hypothetical protein -
lmonocytogenes MJKNJD_006 2938 3627 + - Ribonuclease 3 -
lmonocytogenes MJKNJD_007 3650 3796 + - hypothetical protein -
lmonocytogenes MJKNJD_008 3747 3920 + - hypothetical protein -
lmonocytogenes MJKNJD_009 5361 5765 + - hypothetical protein -
lmonocytogenes MJKNJD_010 5707 6819 + - Tyrosine-protein phosphatase -
lmonocytogenes MJKNJD_011 7714 8049 - - hypothetical protein -
lmonocytogenes MJKNJD_012 9053 9316 + khpA RNA-binding protein KhpA -
lmonocytogenes MJKNJD_013 9390 10127 + - Peptidase C26 -
lmonocytogenes MJKNJD_014 10155 10541 + ylqD YlqD protein -
lmonocytogenes MJKNJD_015 10595 10786 + - hypothetical protein -
lmonocytogenes MJKNJD_016 10875 11201 - - hypothetical protein -
lmonocytogenes MJKNJD_017 11473 11634 + - hypothetical protein -
lmonocytogenes MJKNJD_018 13304 13557 + rli43 Listeria sRNA rli43 -
lmonocytogenes MJKNJD_019 13790 14362 + - hypothetical protein -
lmonocytogenes MJKNJD_020 14451 14786 + - hypothetical protein -
lmonocytogenes MJKNJD_021 15932 16240 - - hypothetical protein -
lmonocytogenes MJKNJD_022 17251 18605 + rrs 16S ribosomal RNA -
lmonocytogenes MJKNJD_023 18842 21611 + rrl 23S ribosomal RNA -
lmonocytogenes MJKNJD_024 21690 21803 + rrf 5S ribosomal RNA -
lmonocytogenes MJKNJD_025 21929 22126 + - hypothetical protein -
lmonocytogenes MJKNJD_026 22165 22542 + - hypothetical protein -
lmonocytogenes MJKNJD_027 22648 23133 + - N5-carboxyaminoimidazole ribonucleotide mutase -
lmonocytogenes MJKNJD_028 23117 23686 + - hypothetical protein -
lmonocytogenes MJKNJD_029 23628 24245 + - hypothetical protein -
lmonocytogenes MJKNJD_030 24264 24584 + - hypothetical protein -
lmonocytogenes MJKNJD_031 24556 25005 + - hypothetical protein -
lmonocytogenes MJKNJD_032 25007 25237 + - hypothetical protein -
lmonocytogenes MJKNJD_033 25234 25557 + - hypothetical protein -
lmonocytogenes MJKNJD_034 25638 26351 + - Phosphoribosylaminoimidazole-succinocarboxamide synthase -
lmonocytogenes MJKNJD_035 26363 26497 + - hypothetical protein -
lmonocytogenes MJKNJD_036 26469 26606 + - hypothetical protein -
lmonocytogenes MJKNJD_037 26610 26786 + - hypothetical protein -
lmonocytogenes MJKNJD_038 27001 28020 + purL Phosphoribosylformylglycinamidine synthase subunit PurL -
lmonocytogenes MJKNJD_039 27995 29221 + - hypothetical protein -
lmonocytogenes MJKNJD_040 29206 30321 + - hypothetical protein -
lmonocytogenes MJKNJD_041 30269 30661 + - hypothetical protein -
lmonocytogenes MJKNJD_042 30642 30731 + - hypothetical protein -
lmonocytogenes MJKNJD_043 31031 31147 + - hypothetical protein -
lmonocytogenes MJKNJD_044 32254 32529 - - hypothetical protein -
lmonocytogenes MJKNJD_045 33306 33419 + - hypothetical protein -
lmonocytogenes MJKNJD_046 36880 37068 + - hypothetical protein -
lmonocytogenes MJKNJD_047 37241 37444 + - hypothetical protein -
lmonocytogenes MJKNJD_048 37570 37887 + - hypothetical protein -
lmonocytogenes MJKNJD_049 38536 38880 + - hypothetical protein -
lmonocytogenes MJKNJD_050 38834 39133 + - hypothetical protein -
lmonocytogenes MJKNJD_051 39307 40062 + - Secreted protein -
lmonocytogenes MJKNJD_052 40086 41135 + - hypothetical protein -
lmonocytogenes MJKNJD_053 41089 41442 + - hypothetical protein -
lmonocytogenes MJKNJD_054 41770 42330 + - Molybdate metabolism regulator -
lmonocytogenes MJKNJD_055 42361 42834 - - Shikimate kinase -
lmonocytogenes MJKNJD_056 43057 43317 + - hypothetical protein -
lmonocytogenes MJKNJD_057 43367 43558 + - hypothetical protein -
lmonocytogenes MJKNJD_058 43719 44213 + - ABC transporter ATP-binding protein -
lmonocytogenes MJKNJD_059 44237 44428 + - hypothetical protein -
lmonocytogenes MJKNJD_060 44824 45345 + - hypothetical protein -
lmonocytogenes MJKNJD_061 45351 45584 + - hypothetical protein -
lmonocytogenes MJKNJD_062 46502 46669 + - hypothetical protein -
lmonocytogenes MJKNJD_063 46786 46935 + - hypothetical protein -
lmonocytogenes MJKNJD_064 47005 47451 + - hypothetical protein -
lmonocytogenes MJKNJD_065 47472 47675 + - hypothetical protein -
lmonocytogenes MJKNJD_066 48908 49090 + - hypothetical protein -
lmonocytogenes MJKNJD_067 49233 50003 + - hypothetical protein -
lmonocytogenes MJKNJD_068 49954 50274 + - hypothetical protein -
lmonocytogenes MJKNJDDNGJ_5 50373 50613 + - T-box leader -
lmonocytogenes MJKNJD_069 50666 50914 + - hypothetical protein -
lmonocytogenes MJKNJD_070 50919 51308 + - hypothetical protein -
lmonocytogenes MJKNJD_071 51319 51603 + - hypothetical protein -
lmonocytogenes MJKNJD_072 51908 52024 + - hypothetical protein -
lmonocytogenes MJKNJD_073 52401 52628 - - hypothetical protein -
lmonocytogenes MJKNJD_074 53282 53542 + - hypothetical protein -
lmonocytogenes MJKNJD_075 54673 54846 + - hypothetical protein -
lmonocytogenes MJKNJD_076 55514 55699 - - hypothetical protein -
lmonocytogenes MJKNJD_077 56116 56376 + - hypothetical protein -
lmonocytogenes MJKNJD_078 58678 59493 + - ABC transporter, permease protein -
lmonocytogenes MJKNJD_079 59536 59712 + - hypothetical protein -
lmonocytogenes MJKNJD_080 59692 60018 - - hypothetical protein -
lmonocytogenes MJKNJD_081 60009 60197 - - hypothetical protein -

Antimicrobial resistance prediction

The assembly was analysed for presence of antimicrobial resistance genes and mutations using ResFinder.
You can use the dropdown menu to select different samples.

No AMR genes or mutations detected for this sample.
No AMR genes or mutations detected for this sample.

Multilocus sequence typing

Multilocus sequencing typing was performed using MLST. Typing scheme information is available at PubMLST.
You can use the dropdown menu to select different samples.

MLST was unable to identify scheme for this sample. Please check coverage of sample.
MLST was unable to identify scheme for this sample. Please check coverage of sample.

Genome coverage

The plot below illustrates depth of coverage. For adequate variant calling, depth should be at least 50X in any region.
Use the dropdown menu to select different samples.

Coverage for up to 20 longest contigs is displayed for each sample.

Software versions

Name Version
bakta 1.11.3
medaka 2.2.0
bcftools 1.21
mlst 2.23.0
sourmash 4.9.4
mob_recon 3.1.9
resfinder 4.7.2
SeqSero2 1.2.1
pysam 0.23.3
fastcat 0.22.1
bamstats 0.22.1
mosdepth 0.3.11
flye 2.9.5-b1801
dnaapler 1.2.0
pomoxis 0.3.16

Workflow parameters

Key Value
out_dir wf-bacterial-genomes
store_dir wf-bacterial-genomes/store_dir
fastq test_data/fastq
reference_based_assembly True
reference test_data/ref/reference.subseq.fa.gz
threads 4
chunk_size 100000
bam None
client_fields None
run_bakta True
bakta_opts None
bakta_db None
bakta_db_type light
sample None
sample_sheet None
override_basecaller_cfg None
min_read_length 1000
max_coverage_plots 20
flye_opts None
flye_genome_size None
flye_asm_coverage None
run_plasmid_id True
plasmid_id_opts None
isolates True
resfinder_threshold 0.8
resfinder_coverage 0.6
pointfinder_ignore_indels False
pointfinder_ignore_stop_codons False
resfinder_db None
pointfinder_db None
analyse_unclassified False
_sourmash_db_exclude_list /builds/oss2rghB/0/epi2melabs/workflows/wf-bacterial-genomes/./data/sourmash_db_exclude_list.txt
_sourmash_pointfinder_mapping /builds/oss2rghB/0/epi2melabs/workflows/wf-bacterial-genomes/./data/pointfinder_db_mapping.csv