Read summary
Genome coverage
The plot below illustrates depth of coverage. For adequate variant calling, depth should be at least 50X in any region. There will be several plots if there were multiple references. Use the dropdown menu to select different samples.
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 tranversions:
| 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. You can select different samples from the dropdown menu.
Annotations
The contigs were annotated with Prokka. You can use the dropdown menu to select different samples.| Contig | ID | Start | End | Strand | Gene | Product | EC number |
|---|---|---|---|---|---|---|---|
| lmonocytogenes | HFJKPDKE_00001 | 49 | 492 | + | mfd | Transcription-repair-coupling factor | 3.6.4.- |
| lmonocytogenes | HFJKPDKE_00002 | 431 | 601 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00003 | 763 | 1242 | + | fapR | Transcription factor FapR | - |
| lmonocytogenes | HFJKPDKE_00004 | 2510 | 2743 | + | acpA | Acyl carrier protein | - |
| lmonocytogenes | HFJKPDKE_00005 | 2938 | 3627 | + | rnc | Ribonuclease 3 | 3.1.26.3 |
| lmonocytogenes | HFJKPDKE_00006 | 3650 | 3796 | + | smc_1 | Chromosome partition protein Smc | - |
| lmonocytogenes | HFJKPDKE_00007 | 3747 | 3920 | + | smc_2 | Chromosome partition protein Smc | - |
| lmonocytogenes | HFJKPDKE_00008 | 5361 | 5765 | + | ffh | Signal recognition particle protein | - |
| lmonocytogenes | HFJKPDKE_00009 | 5908 | 6819 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00010 | 8593 | 9015 | - | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00011 | 9053 | 9316 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00012 | 9393 | 10127 | + | puuD | Gamma-glutamyl-gamma-aminobutyrate hydrolase PuuD | 3.5.1.94 |
| lmonocytogenes | HFJKPDKE_00013 | 10155 | 10541 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00014 | 13838 | 14362 | + | inlC | Internalin C | - |
| lmonocytogenes | HFJKPDKE_00015 | 14451 | 14786 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00016 | 15129 | 15401 | - | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00017 | 16986 | 17225 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00018 | 17844 | 18604 | + | - | 16S ribosomal RNA (partial) | - |
| lmonocytogenes | HFJKPDKE_00019 | 18844 | 21609 | + | - | 23S ribosomal RNA | - |
| lmonocytogenes | HFJKPDKE_00020 | 21693 | 21799 | + | - | 5S ribosomal RNA | - |
| lmonocytogenes | HFJKPDKE_00021 | 21929 | 22126 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00022 | 22165 | 22542 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00023 | 22648 | 23133 | + | purE | N5-carboxyaminoimidazole ribonucleotide mutase | 5.4.99.18 |
| lmonocytogenes | HFJKPDKE_00024 | 23117 | 23686 | + | purK_1 | N5-carboxyaminoimidazole ribonucleotide synthase | 6.3.4.18 |
| lmonocytogenes | HFJKPDKE_00025 | 23700 | 24245 | + | purK_2 | N5-carboxyaminoimidazole ribonucleotide synthase | 6.3.4.18 |
| lmonocytogenes | HFJKPDKE_00026 | 24264 | 24584 | + | purB_1 | Adenylosuccinate lyase | 4.3.2.2 |
| lmonocytogenes | HFJKPDKE_00027 | 24556 | 25005 | + | purB_2 | Adenylosuccinate lyase | 4.3.2.2 |
| lmonocytogenes | HFJKPDKE_00028 | 25007 | 25237 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00029 | 25255 | 25557 | + | purB_3 | Adenylosuccinate lyase | 4.3.2.2 |
| lmonocytogenes | HFJKPDKE_00030 | 25638 | 26351 | + | purC | Phosphoribosylaminoimidazole-succinocarboxamide synthase | 6.3.2.6 |
| lmonocytogenes | HFJKPDKE_00031 | 26363 | 26497 | + | purS | Phosphoribosylformylglycinamidine synthase subunit PurS | 6.3.5.3 |
| lmonocytogenes | HFJKPDKE_00032 | 26469 | 26606 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00033 | 26610 | 26786 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00034 | 27001 | 28020 | + | purL_1 | Phosphoribosylformylglycinamidine synthase subunit PurL | 6.3.5.3 |
| lmonocytogenes | HFJKPDKE_00035 | 27995 | 29221 | + | purL_2 | Phosphoribosylformylglycinamidine synthase subunit PurL | 6.3.5.3 |
| lmonocytogenes | HFJKPDKE_00036 | 29206 | 30321 | + | purF_1 | Amidophosphoribosyltransferase | 2.4.2.14 |
| lmonocytogenes | HFJKPDKE_00037 | 30269 | 30661 | + | purF_2 | Amidophosphoribosyltransferase | 2.4.2.14 |
| lmonocytogenes | HFJKPDKE_00038 | 30558 | 31028 | - | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00039 | 31031 | 31147 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00040 | 31571 | 31846 | - | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00041 | 32254 | 32529 | - | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00042 | 33306 | 33419 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00043 | 35415 | 35537 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00044 | 36880 | 37068 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00045 | 37241 | 37444 | + | gatA | Glutamyl-tRNA(Gln) amidotransferase subunit A | 6.3.5.7 |
| lmonocytogenes | HFJKPDKE_00046 | 37570 | 37887 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00047 | 38536 | 38880 | + | dagK_1 | Diacylglycerol kinase | 2.7.1.107 |
| lmonocytogenes | HFJKPDKE_00048 | 38834 | 39133 | + | dagK_2 | Diacylglycerol kinase | 2.7.1.107 |
| lmonocytogenes | HFJKPDKE_00049 | 39307 | 40062 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00050 | 40086 | 41135 | + | rlmCD_1 | 23S rRNA (uracil-C(5))-methyltransferase RlmCD | 2.1.1.189 |
| lmonocytogenes | HFJKPDKE_00051 | 41089 | 41442 | + | rlmCD_2 | 23S rRNA (uracil-C(5))-methyltransferase RlmCD | 2.1.1.189 |
| lmonocytogenes | HFJKPDKE_00052 | 41776 | 42330 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00053 | 42361 | 42834 | - | aroK | Shikimate kinase | 2.7.1.71 |
| lmonocytogenes | HFJKPDKE_00054 | 43057 | 43317 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00055 | 43367 | 43558 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00056 | 43779 | 44213 | + | bceA | Bacitracin export ATP-binding protein BceA | - |
| lmonocytogenes | HFJKPDKE_00057 | 44255 | 44428 | + | yxdL | ABC transporter ATP-binding protein YxdL | - |
| lmonocytogenes | HFJKPDKE_00058 | 44475 | 44609 | - | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00059 | 44824 | 45345 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00060 | 45351 | 45584 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00061 | 46502 | 46669 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00062 | 46786 | 46935 | + | graR | Response regulator protein GraR | - |
| lmonocytogenes | HFJKPDKE_00063 | 47005 | 47451 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00064 | 47472 | 47675 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00065 | 48352 | 48462 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00066 | 48908 | 49090 | + | ade | Adenine deaminase | 3.5.4.2 |
| lmonocytogenes | HFJKPDKE_00067 | 49233 | 50003 | + | graS_1 | Sensor histidine kinase GraS | 2.7.13.3 |
| lmonocytogenes | HFJKPDKE_00068 | 49954 | 50274 | + | graS_2 | Sensor histidine kinase GraS | 2.7.13.3 |
| lmonocytogenes | HFJKPDKE_00069 | 50666 | 50914 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00070 | 50919 | 51308 | + | artQ | Arginine transport system permease protein ArtQ | - |
| lmonocytogenes | HFJKPDKE_00071 | 51319 | 51603 | + | tcyN | L-cystine import ATP-binding protein TcyN | 3.6.3.- |
| lmonocytogenes | HFJKPDKE_00072 | 53282 | 53542 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00073 | 53648 | 53791 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00074 | 55099 | 55269 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00075 | 55514 | 55699 | - | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00076 | 56116 | 56376 | + | - | 1%2C2-beta-oligoglucan phosphorylase | 2.4.1.333 |
| lmonocytogenes | HFJKPDKE_00077 | 57612 | 57812 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00078 | 58720 | 59493 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00079 | 59536 | 59712 | + | - | hypothetical protein | - |
| lmonocytogenes | HFJKPDKE_00080 | 59692 | 60243 | - | - | hypothetical protein | - |
| Contig | ID | Start | End | Strand | Gene | Product | EC number |
|---|---|---|---|---|---|---|---|
| lmonocytogenes | NLKGMCLA_00001 | 49 | 156 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00002 | 174 | 578 | + | recG | ATP-dependent DNA helicase RecG | 3.6.4.12 |
| lmonocytogenes | NLKGMCLA_00003 | 2474 | 2590 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00004 | 2580 | 2843 | + | rnc | Ribonuclease 3 | 3.1.26.3 |
| lmonocytogenes | NLKGMCLA_00005 | 2952 | 3365 | - | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00006 | 6409 | 6546 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00007 | 9680 | 9901 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00008 | 10032 | 10490 | - | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00009 | 10528 | 10833 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00010 | 11225 | 11635 | - | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00011 | 11706 | 12290 | - | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00012 | 12574 | 12843 | - | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00013 | 13507 | 13953 | + | inlC_1 | Internalin C | - |
| lmonocytogenes | NLKGMCLA_00014 | 13988 | 14401 | + | inlC_2 | Internalin C | - |
| lmonocytogenes | NLKGMCLA_00015 | 15594 | 15890 | - | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00016 | 16508 | 17338 | + | - | 16S ribosomal RNA (partial) | - |
| lmonocytogenes | NLKGMCLA_00017 | 17583 | 20300 | + | - | 23S ribosomal RNA | - |
| lmonocytogenes | NLKGMCLA_00018 | 20620 | 20730 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00019 | 21546 | 21680 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00020 | 22328 | 22546 | + | purB | Adenylosuccinate lyase | 4.3.2.2 |
| lmonocytogenes | NLKGMCLA_00021 | 22531 | 22749 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00022 | 24819 | 25019 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00023 | 25035 | 25526 | + | purF_1 | Amidophosphoribosyltransferase | 2.4.2.14 |
| lmonocytogenes | NLKGMCLA_00024 | 25604 | 26008 | + | purF_2 | Amidophosphoribosyltransferase | 2.4.2.14 |
| lmonocytogenes | NLKGMCLA_00025 | 26005 | 26376 | + | purF_3 | Amidophosphoribosyltransferase | 2.4.2.14 |
| lmonocytogenes | NLKGMCLA_00026 | 26395 | 26640 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00027 | 27119 | 27454 | + | purN | Phosphoribosylglycinamide formyltransferase | 2.1.2.2 |
| lmonocytogenes | NLKGMCLA_00028 | 27700 | 27843 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00029 | 28085 | 28390 | + | purH_1 | Bifunctional purine biosynthesis protein PurH | - |
| lmonocytogenes | NLKGMCLA_00030 | 28417 | 28719 | + | purH_2 | Bifunctional purine biosynthesis protein PurH | - |
| lmonocytogenes | NLKGMCLA_00031 | 28885 | 29226 | + | purH_3 | Bifunctional purine biosynthesis protein PurH | - |
| lmonocytogenes | NLKGMCLA_00032 | 29251 | 29757 | + | purD_1 | Phosphoribosylamine--glycine ligase | 6.3.4.13 |
| lmonocytogenes | NLKGMCLA_00033 | 29851 | 30492 | + | purD_2 | Phosphoribosylamine--glycine ligase | 6.3.4.13 |
| lmonocytogenes | NLKGMCLA_00034 | 30607 | 30795 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00035 | 30743 | 30928 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00036 | 31261 | 31545 | - | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00037 | 34692 | 34880 | + | ligA | DNA ligase | 6.5.1.2 |
| lmonocytogenes | NLKGMCLA_00038 | 35338 | 35514 | - | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00039 | 36542 | 36835 | + | GATC | Glutamyl-tRNA(Gln) amidotransferase subunit C%2C chloroplastic/mitochondrial | 6.3.5.- |
| lmonocytogenes | NLKGMCLA_00040 | 37058 | 37708 | + | gatA | Glutamyl-tRNA(Gln) amidotransferase subunit A | 6.3.5.7 |
| lmonocytogenes | NLKGMCLA_00041 | 38776 | 38913 | + | dagK | Diacylglycerol kinase | 2.7.1.107 |
| lmonocytogenes | NLKGMCLA_00042 | 38940 | 39200 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00043 | 39348 | 39485 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00044 | 39518 | 40105 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00045 | 40129 | 40401 | + | rlmD | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | 2.1.1.190 |
| lmonocytogenes | NLKGMCLA_00046 | 40607 | 41125 | + | rlmCD | 23S rRNA (uracil-C(5))-methyltransferase RlmCD | 2.1.1.189 |
| lmonocytogenes | NLKGMCLA_00047 | 41562 | 42113 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00048 | 43122 | 43274 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00049 | 43319 | 44101 | + | bceA | Bacitracin export ATP-binding protein BceA | - |
| lmonocytogenes | NLKGMCLA_00050 | 44091 | 44627 | + | bceB | Bacitracin export permease protein BceB | - |
| lmonocytogenes | NLKGMCLA_00051 | 44581 | 45825 | + | yxdM | ABC transporter permease protein YxdM | - |
| lmonocytogenes | NLKGMCLA_00052 | 45914 | 46066 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00053 | 46132 | 46554 | + | graR_1 | Response regulator protein GraR | - |
| lmonocytogenes | NLKGMCLA_00054 | 46610 | 46810 | + | graR_2 | Response regulator protein GraR | - |
| lmonocytogenes | NLKGMCLA_00055 | 46880 | 47755 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00056 | 47775 | 48020 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00057 | 49476 | 50159 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00058 | 50163 | 50519 | + | rcsD | Phosphotransferase RcsD | 2.7.2.- |
| lmonocytogenes | NLKGMCLA_00059 | 50917 | 51420 | + | yecS | L-cystine transport system permease protein YecS | - |
| lmonocytogenes | NLKGMCLA_00060 | 51438 | 51557 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00061 | 51568 | 51840 | + | btuD | Vitamin B12 import ATP-binding protein BtuD | 7.6.2.8 |
| lmonocytogenes | NLKGMCLA_00062 | 51786 | 51944 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00063 | 51962 | 52219 | + | artM | Arginine transport ATP-binding protein ArtM | - |
| lmonocytogenes | NLKGMCLA_00064 | 52221 | 52592 | + | fliY | L-cystine-binding protein FliY | - |
| lmonocytogenes | NLKGMCLA_00065 | 52642 | 52812 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00066 | 53223 | 53429 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00067 | 54815 | 55036 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00068 | 55118 | 55603 | - | araQ | L-arabinose transport system permease protein AraQ | - |
| lmonocytogenes | NLKGMCLA_00069 | 55554 | 55748 | - | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00070 | 56740 | 56997 | - | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00071 | 57093 | 57404 | - | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00072 | 57590 | 57826 | - | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00073 | 57838 | 57948 | - | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00074 | 58163 | 58375 | - | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00075 | 59403 | 59543 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00076 | 60348 | 60608 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00077 | 60861 | 61109 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00078 | 61152 | 61337 | + | - | hypothetical protein | - |
| lmonocytogenes | NLKGMCLA_00079 | 61309 | 61860 | - | - | hypothetical protein | - |