Read summary

Number of reads

Number of reads after applying read length and quality filters. Read counts will also reflect host depletion and unclassified reads (kraken2 approach) and unmapped reads (minimap2 approach). Percentages are calculated from reads after the filtering.

Note that in the minimap2 approach, there are two filters based on the mapping identity and coverage that can increase the number of unclassified sequences. This table shows the unmapped reads before both filters are applied.

index Reads Unclassified|Unmapped Unclassified|Unmapped (%)
barcode01 7838.0 0.0 0.0
barcode02 3927.0 0.0 0.0
barcode03 3913.0 0.0 0.0

Lineages

Sunburst

This visualization can be useful to interactively explore the taxonomic composition of the sample. It shows hierarchical data: each layer represents a taxonomic rank. The color indicates the abundance of that taxon in comparison with the total number of reads. Zooming into an specific taxon is possible by clicking on it.

This visualization can be useful to interactively explore the taxonomic composition of the sample. It shows hierarchical data: each layer represents a taxonomic rank. The color indicates the abundance of that taxon in comparison with the total number of reads. Zooming into an specific taxon is possible by clicking on it.

This visualization can be useful to interactively explore the taxonomic composition of the sample. It shows hierarchical data: each layer represents a taxonomic rank. The color indicates the abundance of that taxon in comparison with the total number of reads. Zooming into an specific taxon is possible by clicking on it.

Taxonomy

Barplot of the 9 most abundant taxa at the phylum rank in all the samples. Any remaining taxa have been collapsed under the 'Other' category to facilitate the visualization. The y-axis indicates the relative abundance of each taxon in percentages for each sample.

Barplot of the 9 most abundant taxa at the class rank in all the samples. Any remaining taxa have been collapsed under the 'Other' category to facilitate the visualization. The y-axis indicates the relative abundance of each taxon in percentages for each sample.

Barplot of the 9 most abundant taxa at the order rank in all the samples. Any remaining taxa have been collapsed under the 'Other' category to facilitate the visualization. The y-axis indicates the relative abundance of each taxon in percentages for each sample.

Barplot of the 9 most abundant taxa at the family rank in all the samples. Any remaining taxa have been collapsed under the 'Other' category to facilitate the visualization. The y-axis indicates the relative abundance of each taxon in percentages for each sample.

Barplot of the 9 most abundant taxa at the genus rank in all the samples. Any remaining taxa have been collapsed under the 'Other' category to facilitate the visualization. The y-axis indicates the relative abundance of each taxon in percentages for each sample.

Abundances

Abundance table for the phylum rank.

Only taxa whose global abundance are above the abundance_threshold parameter will appear in the table.

phylum barcode01 barcode02 barcode03 total superkingdom kingdom tax
Bacillota 4842.0 2349.0 2493.0 9684.0 Bacteria Bacillati Bacteria;Bacillati;Bacillota
Fusobacteriota 206.0 73.0 109.0 388.0 Bacteria Fusobacteriati Bacteria;Fusobacteriati;Fusobacteriota
Bacteroidota 279.0 121.0 125.0 525.0 Bacteria Pseudomonadati Bacteria;Pseudomonadati;Bacteroidota
Pseudomonadota 2116.0 1187.0 979.0 4282.0 Bacteria Pseudomonadati Bacteria;Pseudomonadati;Pseudomonadota
Verrucomicrobiota 19.0 1.0 15.0 35.0 Bacteria Pseudomonadati Bacteria;Pseudomonadati;Verrucomicrobiota
Unknown 376.0 196.0 192.0 764.0 Unclassified Unknown Unclassified;Unknown;Unknown

Abundance table for the class rank.

Only taxa whose global abundance are above the abundance_threshold parameter will appear in the table.

class barcode01 barcode02 barcode03 total superkingdom kingdom phylum tax
Bacilli 142.0 86.0 94.0 322.0 Bacteria Bacillati Bacillota Bacteria;Bacillati;Bacillota;Bacilli
Clostridia 2324.0 1216.0 1016.0 4556.0 Bacteria Bacillati Bacillota Bacteria;Bacillati;Bacillota;Clostridia
Negativicutes 2376.0 1047.0 1383.0 4806.0 Bacteria Bacillati Bacillota Bacteria;Bacillati;Bacillota;Negativicutes
Fusobacteriia 206.0 73.0 109.0 388.0 Bacteria Fusobacteriati Fusobacteriota Bacteria;Fusobacteriati;Fusobacteriota;Fusobacteriia
Bacteroidia 279.0 121.0 125.0 525.0 Bacteria Pseudomonadati Bacteroidota Bacteria;Pseudomonadati;Bacteroidota;Bacteroidia
Betaproteobacteria 1.0 1.0 0.0 2.0 Bacteria Pseudomonadati Pseudomonadota Bacteria;Pseudomonadati;Pseudomonadota;Betaproteobacteria
Gammaproteobacteria 2115.0 1186.0 979.0 4280.0 Bacteria Pseudomonadati Pseudomonadota Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria
Verrucomicrobiia 19.0 1.0 15.0 35.0 Bacteria Pseudomonadati Verrucomicrobiota Bacteria;Pseudomonadati;Verrucomicrobiota;Verrucomicrobiia
Unknown 376.0 196.0 192.0 764.0 Unclassified Unknown Unknown Unclassified;Unknown;Unknown;Unknown

Abundance table for the order rank.

Only taxa whose global abundance are above the abundance_threshold parameter will appear in the table.

order barcode01 barcode02 barcode03 total superkingdom kingdom phylum class tax
Lactobacillales 142.0 86.0 94.0 322.0 Bacteria Bacillati Bacillota Bacilli Bacteria;Bacillati;Bacillota;Bacilli;Lactobacillales
Eubacteriales 1441.0 853.0 644.0 2938.0 Bacteria Bacillati Bacillota Clostridia Bacteria;Bacillati;Bacillota;Clostridia;Eubacteriales
Lachnospirales 376.0 139.0 157.0 672.0 Bacteria Bacillati Bacillota Clostridia Bacteria;Bacillati;Bacillota;Clostridia;Lachnospirales
Peptostreptococcales 507.0 224.0 215.0 946.0 Bacteria Bacillati Bacillota Clostridia Bacteria;Bacillati;Bacillota;Clostridia;Peptostreptococcales
Veillonellales 2376.0 1047.0 1383.0 4806.0 Bacteria Bacillati Bacillota Negativicutes Bacteria;Bacillati;Bacillota;Negativicutes;Veillonellales
Fusobacteriales 206.0 73.0 109.0 388.0 Bacteria Fusobacteriati Fusobacteriota Fusobacteriia Bacteria;Fusobacteriati;Fusobacteriota;Fusobacteriia;Fusobacteriales
Bacteroidales 279.0 121.0 125.0 525.0 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteria;Pseudomonadati;Bacteroidota;Bacteroidia;Bacteroidales
Burkholderiales 1.0 1.0 0.0 2.0 Bacteria Pseudomonadati Pseudomonadota Betaproteobacteria Bacteria;Pseudomonadati;Pseudomonadota;Betaproteobacteria;Burkholderiales
Enterobacterales 2115.0 1186.0 978.0 4279.0 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales
Verrucomicrobiales 19.0 1.0 15.0 35.0 Bacteria Pseudomonadati Verrucomicrobiota Verrucomicrobiia Bacteria;Pseudomonadati;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales
Unknown 376.0 196.0 192.0 764.0 Unclassified Unknown Unknown Unknown Unclassified;Unknown;Unknown;Unknown;Unknown

Abundance table for the family rank.

Only taxa whose global abundance are above the abundance_threshold parameter will appear in the table.

family barcode01 barcode02 barcode03 total superkingdom kingdom phylum class order tax
Lactobacillaceae 142.0 86.0 94.0 322.0 Bacteria Bacillati Bacillota Bacilli Lactobacillales Bacteria;Bacillati;Bacillota;Bacilli;Lactobacillales;Lactobacillaceae
Oscillospiraceae 1441.0 853.0 644.0 2938.0 Bacteria Bacillati Bacillota Clostridia Eubacteriales Bacteria;Bacillati;Bacillota;Clostridia;Eubacteriales;Oscillospiraceae
Lachnospiraceae 376.0 139.0 157.0 672.0 Bacteria Bacillati Bacillota Clostridia Lachnospirales Bacteria;Bacillati;Bacillota;Clostridia;Lachnospirales;Lachnospiraceae
Peptostreptococcaceae 507.0 224.0 215.0 946.0 Bacteria Bacillati Bacillota Clostridia Peptostreptococcales Bacteria;Bacillati;Bacillota;Clostridia;Peptostreptococcales;Peptostreptococcaceae
Veillonellaceae 2376.0 1047.0 1383.0 4806.0 Bacteria Bacillati Bacillota Negativicutes Veillonellales Bacteria;Bacillati;Bacillota;Negativicutes;Veillonellales;Veillonellaceae
Fusobacteriaceae 206.0 73.0 109.0 388.0 Bacteria Fusobacteriati Fusobacteriota Fusobacteriia Fusobacteriales Bacteria;Fusobacteriati;Fusobacteriota;Fusobacteriia;Fusobacteriales;Fusobacteriaceae
Bacteroidaceae 157.0 64.0 53.0 274.0 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteria;Pseudomonadati;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae
Prevotellaceae 122.0 57.0 72.0 251.0 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteria;Pseudomonadati;Bacteroidota;Bacteroidia;Bacteroidales;Prevotellaceae
Burkholderiaceae 1.0 1.0 0.0 2.0 Bacteria Pseudomonadati Pseudomonadota Betaproteobacteria Burkholderiales Bacteria;Pseudomonadati;Pseudomonadota;Betaproteobacteria;Burkholderiales;Burkholderiaceae
Enterobacteriaceae 2115.0 1186.0 978.0 4279.0 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae
Akkermansiaceae 19.0 1.0 15.0 35.0 Bacteria Pseudomonadati Verrucomicrobiota Verrucomicrobiia Verrucomicrobiales Bacteria;Pseudomonadati;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales;Akkermansiaceae
Unknown 376.0 196.0 192.0 764.0 Unclassified Unknown Unknown Unknown Unknown Unclassified;Unknown;Unknown;Unknown;Unknown;Unknown

Abundance table for the genus rank.

Only taxa whose global abundance are above the abundance_threshold parameter will appear in the table.

genus barcode01 barcode02 barcode03 total superkingdom kingdom phylum class order family tax
Limosilactobacillus 142.0 86.0 94.0 322.0 Bacteria Bacillati Bacillota Bacilli Lactobacillales Lactobacillaceae Bacteria;Bacillati;Bacillota;Bacilli;Lactobacillales;Lactobacillaceae;Limosilactobacillus
Faecalibacterium 1441.0 853.0 644.0 2938.0 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Bacteria;Bacillati;Bacillota;Clostridia;Eubacteriales;Oscillospiraceae;Faecalibacterium
Roseburia 376.0 139.0 157.0 672.0 Bacteria Bacillati Bacillota Clostridia Lachnospirales Lachnospiraceae Bacteria;Bacillati;Bacillota;Clostridia;Lachnospirales;Lachnospiraceae;Roseburia
Clostridioides 507.0 224.0 215.0 946.0 Bacteria Bacillati Bacillota Clostridia Peptostreptococcales Peptostreptococcaceae Bacteria;Bacillati;Bacillota;Clostridia;Peptostreptococcales;Peptostreptococcaceae;Clostridioides
Veillonella 2376.0 1047.0 1383.0 4806.0 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Bacteria;Bacillati;Bacillota;Negativicutes;Veillonellales;Veillonellaceae;Veillonella
Fusobacterium 206.0 73.0 109.0 388.0 Bacteria Fusobacteriati Fusobacteriota Fusobacteriia Fusobacteriales Fusobacteriaceae Bacteria;Fusobacteriati;Fusobacteriota;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium
Bacteroides 157.0 64.0 53.0 274.0 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteroidaceae Bacteria;Pseudomonadati;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides
Prevotella 122.0 57.0 72.0 251.0 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Prevotellaceae Bacteria;Pseudomonadati;Bacteroidota;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella
Paraburkholderia 1.0 1.0 0.0 2.0 Bacteria Pseudomonadati Pseudomonadota Betaproteobacteria Burkholderiales Burkholderiaceae Bacteria;Pseudomonadati;Pseudomonadota;Betaproteobacteria;Burkholderiales;Burkholderiaceae;Paraburkholderia
Escherichia 937.0 531.0 452.0 1920.0 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia
Salmonella 1.0 0.0 4.0 5.0 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Salmonella
Shigella 1177.0 655.0 522.0 2354.0 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Shigella
Akkermansia 19.0 1.0 15.0 35.0 Bacteria Pseudomonadati Verrucomicrobiota Verrucomicrobiia Verrucomicrobiales Akkermansiaceae Bacteria;Pseudomonadati;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales;Akkermansiaceae;Akkermansia
Unknown 376.0 196.0 192.0 764.0 Unclassified Unknown Unknown Unknown Unknown Unknown Unclassified;Unknown;Unknown;Unknown;Unknown;Unknown;Unknown

Rarefied abundance table for the phylum rank.

All samples have been randomly subsetted to have the same number of reads.

phylum barcode01 barcode02 barcode03 total superkingdom kingdom tax
Bacillota 2284 2234 2377 2261 Bacteria Bacillati Bacteria;Bacillati;Bacillota
Fusobacteriota 99 70 104 91 Bacteria Fusobacteriati Bacteria;Fusobacteriati;Fusobacteriota
Bacteroidota 146 107 119 120 Bacteria Pseudomonadati Bacteria;Pseudomonadati;Bacteroidota
Pseudomonadota 1017 1124 921 1036 Bacteria Pseudomonadati Bacteria;Pseudomonadati;Pseudomonadota
Verrucomicrobiota 9 1 14 12 Bacteria Pseudomonadati Bacteria;Pseudomonadati;Verrucomicrobiota
Unknown 162 181 182 197 Unclassified Unknown Unclassified;Unknown;Unknown

Rarefied abundance table for the class rank.

All samples have been randomly subsetted to have the same number of reads.

class barcode01 barcode02 barcode03 total superkingdom kingdom phylum tax
Bacilli 64 81 87 81 Bacteria Bacillati Bacillota Bacteria;Bacillati;Bacillota;Bacilli
Clostridia 1109 1150 965 1061 Bacteria Bacillati Bacillota Bacteria;Bacillati;Bacillota;Clostridia
Negativicutes 1112 990 1315 1190 Bacteria Bacillati Bacillota Bacteria;Bacillati;Bacillota;Negativicutes
Fusobacteriia 115 69 103 85 Bacteria Fusobacteriati Fusobacteriota Bacteria;Fusobacteriati;Fusobacteriota;Fusobacteriia
Bacteroidia 137 116 114 127 Bacteria Pseudomonadati Bacteroidota Bacteria;Pseudomonadati;Bacteroidota;Bacteroidia
Betaproteobacteria 0 1 0 1 Bacteria Pseudomonadati Pseudomonadota Bacteria;Pseudomonadati;Pseudomonadota;Betaproteobacteria
Gammaproteobacteria 1001 1123 936 970 Bacteria Pseudomonadati Pseudomonadota Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria
Verrucomicrobiia 7 1 15 11 Bacteria Pseudomonadati Verrucomicrobiota Bacteria;Pseudomonadati;Verrucomicrobiota;Verrucomicrobiia
Unknown 172 186 182 191 Unclassified Unknown Unknown Unclassified;Unknown;Unknown;Unknown

Rarefied abundance table for the order rank.

All samples have been randomly subsetted to have the same number of reads.

order barcode01 barcode02 barcode03 total superkingdom kingdom phylum class tax
Lactobacillales 83 82 88 80 Bacteria Bacillati Bacillota Bacilli Bacteria;Bacillati;Bacillota;Bacilli;Lactobacillales
Eubacteriales 684 811 610 711 Bacteria Bacillati Bacillota Clostridia Bacteria;Bacillati;Bacillota;Clostridia;Eubacteriales
Lachnospirales 172 130 150 147 Bacteria Bacillati Bacillota Clostridia Bacteria;Bacillati;Bacillota;Clostridia;Lachnospirales
Peptostreptococcales 237 215 200 231 Bacteria Bacillati Bacillota Clostridia Bacteria;Bacillati;Bacillota;Clostridia;Peptostreptococcales
Veillonellales 1128 984 1323 1131 Bacteria Bacillati Bacillota Negativicutes Bacteria;Bacillati;Bacillota;Negativicutes;Veillonellales
Fusobacteriales 99 70 95 95 Bacteria Fusobacteriati Fusobacteriota Fusobacteriia Bacteria;Fusobacteriati;Fusobacteriota;Fusobacteriia;Fusobacteriales
Bacteroidales 142 112 121 108 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteria;Pseudomonadati;Bacteroidota;Bacteroidia;Bacteroidales
Burkholderiales 0 0 0 2 Bacteria Pseudomonadati Pseudomonadota Betaproteobacteria Bacteria;Pseudomonadati;Pseudomonadota;Betaproteobacteria;Burkholderiales
Enterobacterales 982 1125 929 1019 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales
Verrucomicrobiales 10 1 15 7 Bacteria Pseudomonadati Verrucomicrobiota Verrucomicrobiia Bacteria;Pseudomonadati;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales
Unknown 179 186 185 185 Unclassified Unknown Unknown Unknown Unclassified;Unknown;Unknown;Unknown;Unknown

Rarefied abundance table for the family rank.

All samples have been randomly subsetted to have the same number of reads.

family barcode01 barcode02 barcode03 total superkingdom kingdom phylum class order tax
Lactobacillaceae 65 84 91 68 Bacteria Bacillati Bacillota Bacilli Lactobacillales Bacteria;Bacillati;Bacillota;Bacilli;Lactobacillales;Lactobacillaceae
Oscillospiraceae 679 804 611 688 Bacteria Bacillati Bacillota Clostridia Eubacteriales Bacteria;Bacillati;Bacillota;Clostridia;Eubacteriales;Oscillospiraceae
Lachnospiraceae 172 133 153 161 Bacteria Bacillati Bacillota Clostridia Lachnospirales Bacteria;Bacillati;Bacillota;Clostridia;Lachnospirales;Lachnospiraceae
Peptostreptococcaceae 245 212 201 210 Bacteria Bacillati Bacillota Clostridia Peptostreptococcales Bacteria;Bacillati;Bacillota;Clostridia;Peptostreptococcales;Peptostreptococcaceae
Veillonellaceae 1124 988 1323 1150 Bacteria Bacillati Bacillota Negativicutes Veillonellales Bacteria;Bacillati;Bacillota;Negativicutes;Veillonellales;Veillonellaceae
Fusobacteriaceae 105 72 100 88 Bacteria Fusobacteriati Fusobacteriota Fusobacteriia Fusobacteriales Bacteria;Fusobacteriati;Fusobacteriota;Fusobacteriia;Fusobacteriales;Fusobacteriaceae
Bacteroidaceae 69 60 51 64 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteria;Pseudomonadati;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae
Prevotellaceae 57 52 68 54 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteria;Pseudomonadati;Bacteroidota;Bacteroidia;Bacteroidales;Prevotellaceae
Burkholderiaceae 1 1 0 0 Bacteria Pseudomonadati Pseudomonadota Betaproteobacteria Burkholderiales Bacteria;Pseudomonadati;Pseudomonadota;Betaproteobacteria;Burkholderiales;Burkholderiaceae
Enterobacteriaceae 1019 1127 926 1026 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae
Akkermansiaceae 11 1 15 15 Bacteria Pseudomonadati Verrucomicrobiota Verrucomicrobiia Verrucomicrobiales Bacteria;Pseudomonadati;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales;Akkermansiaceae
Unknown 169 182 177 192 Unclassified Unknown Unknown Unknown Unknown Unclassified;Unknown;Unknown;Unknown;Unknown;Unknown

Rarefied abundance table for the genus rank.

All samples have been randomly subsetted to have the same number of reads.

genus barcode01 barcode02 barcode03 total superkingdom kingdom phylum class order family tax
Limosilactobacillus 65 83 93 79 Bacteria Bacillati Bacillota Bacilli Lactobacillales Lactobacillaceae Bacteria;Bacillati;Bacillota;Bacilli;Lactobacillales;Lactobacillaceae;Limosilactobacillus
Faecalibacterium 700 812 609 733 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Bacteria;Bacillati;Bacillota;Clostridia;Eubacteriales;Oscillospiraceae;Faecalibacterium
Roseburia 172 135 152 156 Bacteria Bacillati Bacillota Clostridia Lachnospirales Lachnospiraceae Bacteria;Bacillati;Bacillota;Clostridia;Lachnospirales;Lachnospiraceae;Roseburia
Clostridioides 232 211 206 218 Bacteria Bacillati Bacillota Clostridia Peptostreptococcales Peptostreptococcaceae Bacteria;Bacillati;Bacillota;Clostridia;Peptostreptococcales;Peptostreptococcaceae;Clostridioides
Veillonella 1151 983 1300 1066 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Bacteria;Bacillati;Bacillota;Negativicutes;Veillonellales;Veillonellaceae;Veillonella
Fusobacterium 98 68 107 83 Bacteria Fusobacteriati Fusobacteriota Fusobacteriia Fusobacteriales Fusobacteriaceae Bacteria;Fusobacteriati;Fusobacteriota;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium
Bacteroides 68 59 50 72 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteroidaceae Bacteria;Pseudomonadati;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides
Prevotella 56 55 70 52 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Prevotellaceae Bacteria;Pseudomonadati;Bacteroidota;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella
Paraburkholderia 1 1 0 2 Bacteria Pseudomonadati Pseudomonadota Betaproteobacteria Burkholderiales Burkholderiaceae Bacteria;Pseudomonadati;Pseudomonadota;Betaproteobacteria;Burkholderiales;Burkholderiaceae;Paraburkholderia
Escherichia 443 508 428 461 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia
Salmonella 0 0 4 0 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Salmonella
Shigella 545 615 502 591 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Shigella
Akkermansia 10 1 14 11 Bacteria Pseudomonadati Verrucomicrobiota Verrucomicrobiia Verrucomicrobiales Akkermansiaceae Bacteria;Pseudomonadati;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales;Akkermansiaceae;Akkermansia
Unknown 175 185 181 192 Unclassified Unknown Unknown Unknown Unknown Unknown Unclassified;Unknown;Unknown;Unknown;Unknown;Unknown;Unknown

Alpha Diversity

Sample diversity indices. Indices are calculated from the original abundance table.

Indices barcode01 barcode02 barcode03 total
Berger Parker index 0.3 0.27 0.35 0.31
Effective number of species 7.45 7.21 7.17 7.36
Fisher's alpha 1.79 1.97 1.98 1.64
Inverse Simpson's index 1.21 1.21 1.24 1.21
Pielou's evenness 0.76 0.77 0.75 0.74
Richness 14.0 13.0 14.0 15.0
Shannon diversity index 2.01 1.98 1.97 2.0
Simpson's index 0.83 0.83 0.81 0.82
Total counts 7838.0 3927.0 3913.0 15678.0
Note that the taxon 'Unknown' is considered as a unique taxon.

Sample-based rarefaction curves to display observed taxa richness. Sample size shows the number of reads sampled from the total amount of reads analyzed during the real time analysis. The Y-axis indicates the number of unique taxa at the last analyzed taxonomic rank in those subsampled reads.

Note that Unknown taxon is considered as a unique taxon.
This plot includes all the counts (except Unknown), before applying any filter threshold based on abundances.
This plot includes all the counts (except Unknown), before applying any filter threshold based on abundances.
This plot includes all the counts (except Unknown), before applying any filter threshold based on abundances.

Alignment Statistics

Only taxa present in the abundance table above the abundance_threshold parameter appear in the table.

genus reference ref length number of reads covbases % coverage mean depth mean baseq mean MAPQ taxid superkingdom kingdom phylum class order family species mean sd depth CV % reads
Escherichia NR_024570.1 1450 1 1424 98.21 0.98 32.0 1.0 562 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia coli 0.98 0.13 0.14 0.01
Escherichia NR_025569.1 1494 1 1446 96.79 0.97 25.1 1.0 208962 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia albertii 0.97 0.18 0.18 0.01
Shigella NR_026331.1 1488 537 1488 100.0 526.39 30.3 8.62 623 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Shigella flexneri 526.39 14.17 0.03 6.85
Shigella NR_026332.1 1487 144 1487 100.0 141.11 30.6 47.3 622 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Shigella dysenteriae 141.11 2.74 0.02 1.84
Escherichia NR_027549.1 1473 55 1473 100.0 52.55 29.9 6.89 585054 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia fergusonii 52.55 4.85 0.09 0.7
Faecalibacterium NR_028961.1 1462 34 1462 100.0 29.42 29.9 5.26 853 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium prausnitzii 29.42 5.05 0.17 0.43
Veillonella NR_041879.1 1375 2 1357 98.69 1.76 28.8 19.5 39778 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella dispar 1.76 0.45 0.26 0.03
Roseburia NR_042008.1 1485 153 1483 99.87 150.1 30.9 4.48 585394 Bacteria Bacillati Bacillota Clostridia Lachnospirales Lachnospiraceae Roseburia hominis 150.1 9.28 0.06 1.95
Akkermansia NR_042817.1 1433 2 1433 100.0 1.97 32.4 1.0 349741 Bacteria Pseudomonadati Verrucomicrobiota Verrucomicrobiia Verrucomicrobiales Akkermansiaceae Akkermansia muciniphila 1.97 0.16 0.08 0.03
Veillonella NR_043332.1 1497 121 1494 99.8 118.65 30.3 2.99 479436 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella parvula 118.65 6.77 0.06 1.54
Veillonella NR_044091.1 1344 251 1344 100.0 246.15 30.6 43.8 423477 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella rogosae 246.15 4.52 0.02 3.2
Akkermansia NR_074436.1 1505 17 1474 97.94 16.47 31.1 23.8 239935 Bacteria Pseudomonadati Verrucomicrobiota Verrucomicrobiia Verrucomicrobiales Akkermansiaceae Akkermansia muciniphila 16.47 2.44 0.15 0.22
Bacteroides NR_074784.2 1529 6 1484 97.06 5.67 24.2 1.0 272559 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteroidaceae Bacteroides fragilis 5.67 1.08 0.19 0.08
Roseburia NR_074809.1 1535 238 1496 97.46 227.61 30.0 18.4 585394 Bacteria Bacillati Bacillota Clostridia Lachnospirales Lachnospiraceae Roseburia hominis 227.61 37.32 0.16 3.04
Escherichia NR_074902.1 1542 790 1508 97.8 753.08 30.4 6.93 585054 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia fergusonii 753.08 120.35 0.16 10.08
Salmonella NR_074910.1 1544 1 1492 96.63 0.97 34.5 1.0 90371 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Salmonella enterica 0.97 0.18 0.19 0.01
Veillonella NR_074980.1 1551 77 1525 98.32 71.5 26.7 1.25 479436 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella parvula 71.5 11.68 0.16 0.98
Shigella NR_104826.1 1530 450 1493 97.58 433.35 30.9 1.47 624 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Shigella sonnei 433.35 70.44 0.16 5.74
Shigella NR_104901.1 1515 89 1484 97.95 85.01 30.4 11.8 621 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Shigella boydii 85.01 12.54 0.15 1.14
Limosilactobacillus NR_104927.1 1502 129 1502 100.0 126.85 31.6 13.1 1613 Bacteria Bacillati Bacillota Bacilli Lactobacillales Lactobacillaceae Limosilactobacillus fermentum 126.85 2.16 0.02 1.65
Clostridioides NR_112172.1 1466 1 1108 75.58 0.76 31.7 14.0 1121308 Bacteria Bacillati Bacillota Clostridia Peptostreptococcales Peptostreptococcaceae Clostridioides difficile 0.76 0.43 0.57 0.01
Escherichia NR_112558.1 1110 1 766 69.01 0.69 27.2 20.0 562 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia coli 0.69 0.46 0.67 0.01
Bacteroides NR_112936.1 1490 121 1490 100.0 118.26 30.7 5.6 817 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteroidaceae Bacteroides fragilis 118.26 2.94 0.02 1.54
Veillonella NR_113031.1 1524 971 1524 100.0 954.58 30.5 3.15 29466 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella parvula 954.58 27.27 0.03 12.39
Prevotella NR_113099.1 1479 132 1479 100.0 129.24 31.0 59.9 28128 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Prevotellaceae Prevotella corporis 129.24 2.76 0.02 1.68
Clostridioides NR_113132.1 1464 533 1464 100.0 521.26 30.3 59.7 1121308 Bacteria Bacillati Bacillota Clostridia Peptostreptococcales Peptostreptococcaceae Clostridioides difficile 521.26 9.48 0.02 6.8
Limosilactobacillus NR_113335.1 1501 16 1501 100.0 15.61 29.5 3.44 1613 Bacteria Bacillati Bacillota Bacilli Lactobacillales Lactobacillaceae Limosilactobacillus fermentum 15.61 0.89 0.06 0.2
Fusobacterium NR_113378.1 1480 173 1480 100.0 170.23 30.4 25.7 76859 Bacteria Fusobacteriati Fusobacteriota Fusobacteriia Fusobacteriales Fusobacteriaceae Fusobacterium animalis 170.23 2.97 0.02 2.21
Veillonella NR_113570.1 1520 36 1506 99.08 32.45 30.6 8.19 1110546 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella tobetsuensis 32.45 4.4 0.14 0.46
Escherichia NR_114042.1 1467 7 1467 100.0 6.78 25.8 1.71 562 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia coli 6.78 0.6 0.09 0.09
Escherichia NR_114079.1 1467 9 1467 100.0 7.92 30.1 7.67 564 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia fergusonii 7.92 1.39 0.18 0.11
Veillonella NR_115355.1 1498 993 1498 100.0 976.98 31.5 7.78 39778 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella dispar 976.98 29.45 0.03 12.67
Fusobacterium NR_117291.1 1441 41 1441 100.0 40.1 30.3 7.83 997347 Bacteria Fusobacteriati Fusobacteriota Fusobacteriia Fusobacteriales Fusobacteriaceae Fusobacterium animalis 40.1 1.17 0.03 0.52
Veillonella NR_117759.1 1345 1 1268 94.28 0.94 31.5 60.0 479436 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella parvula 0.94 0.23 0.25 0.01
Bacteroides NR_119164.1 1436 39 1436 100.0 38.48 30.8 10.9 817 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteroidaceae Bacteroides fragilis 38.48 1.21 0.03 0.5
Veillonella NR_119168.1 1513 3 1078 71.25 1.78 27.5 2.33 479436 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella parvula 1.78 1.32 0.74 0.04
Veillonella NR_119169.1 1513 3 1072 70.85 1.92 31.8 1.0 39778 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella dispar 1.92 1.3 0.68 0.04
Escherichia NR_136472.1 1504 127 1504 100.0 125.36 31.2 5.76 1499973 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia marmotae 125.36 2.17 0.02 1.62
Veillonella NR_163639.1 1532 2 1110 72.45 1.41 20.6 4.0 1911679 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella infantium 1.41 0.89 0.63 0.03
Faecalibacterium NR_178280.1 1466 757 1466 100.0 742.7 30.9 15.3 411483 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium duncaniae 742.7 41.23 0.06 9.66
Paraburkholderia NR_178798.1 1428 1 1410 98.74 0.99 26.3 3.0 1441714 Bacteria Pseudomonadati Pseudomonadota Betaproteobacteria Burkholderiales Burkholderiaceae Paraburkholderia fungorum 0.99 0.11 0.11 0.01
Faecalibacterium NR_178971.1 1381 320 1381 100.0 314.0 31.2 10.6 1851427 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium butyricigenerans 314.0 22.42 0.07 4.08
Faecalibacterium NR_178972.1 1372 12 1372 100.0 11.5 28.8 1.42 1851428 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium longum 11.5 1.37 0.12 0.15
Veillonella NR_179325.1 1469 37 1465 99.73 35.67 29.7 5.43 2682456 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella nakazawae 35.67 2.48 0.07 0.47
Faecalibacterium NR_179388.1 1472 403 1472 100.0 393.34 30.9 22.3 2935520 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium hattorii 393.34 21.88 0.06 5.14

Only taxa present in the abundance table above the abundance_threshold parameter appear in the table.

genus reference ref length number of reads covbases % coverage mean depth mean baseq mean MAPQ taxid superkingdom kingdom phylum class order family species mean sd depth CV % reads
Escherichia NR_025569.1 1494 2 1450 97.05 1.45 30.5 0.5 208962 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia albertii 1.45 0.55 0.38 0.05
Shigella NR_026331.1 1488 303 1488 100.0 297.75 30.7 9.17 623 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Shigella flexneri 297.75 6.72 0.02 7.72
Shigella NR_026332.1 1487 66 1487 100.0 65.27 30.9 48.1 622 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Shigella dysenteriae 65.27 1.17 0.02 1.68
Escherichia NR_027549.1 1473 30 1473 100.0 29.17 30.6 8.17 585054 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia fergusonii 29.17 2.67 0.09 0.76
Faecalibacterium NR_028961.1 1462 18 1461 99.93 15.4 29.8 4.56 853 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium prausnitzii 15.4 3.44 0.22 0.46
Veillonella NR_041879.1 1375 1 1049 76.29 0.76 33.5 12.0 39778 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella dispar 0.76 0.43 0.56 0.03
Roseburia NR_042008.1 1485 58 1480 99.66 57.21 31.6 3.4 585394 Bacteria Bacillati Bacillota Clostridia Lachnospirales Lachnospiraceae Roseburia hominis 57.21 3.56 0.06 1.48
Akkermansia NR_042817.1 1433 1 1427 99.58 1.0 35.8 29.0 349741 Bacteria Pseudomonadati Verrucomicrobiota Verrucomicrobiia Verrucomicrobiales Akkermansiaceae Akkermansia muciniphila 1.0 0.06 0.06 0.03
Veillonella NR_043332.1 1497 51 1494 99.8 50.28 31.0 3.04 479436 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella parvula 50.28 2.89 0.06 1.3
Veillonella NR_044091.1 1344 131 1344 100.0 127.86 30.4 41.8 423477 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella rogosae 127.86 3.29 0.03 3.34
Bacteroides NR_074784.2 1529 3 1483 96.99 2.85 29.1 2.67 272559 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteroidaceae Bacteroides fragilis 2.85 0.57 0.2 0.08
Salmonella NR_074799.1 1534 1 903 58.87 0.59 21.0 5.0 90370 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Salmonella enterica 0.59 0.49 0.84 0.03
Roseburia NR_074809.1 1535 89 1494 97.33 84.21 30.2 18.0 585394 Bacteria Bacillati Bacillota Clostridia Lachnospirales Lachnospiraceae Roseburia hominis 84.21 14.15 0.17 2.27
Escherichia NR_074902.1 1542 469 1508 97.8 448.91 30.5 5.99 585054 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia fergusonii 448.91 71.78 0.16 11.94
Veillonella NR_074980.1 1551 30 1525 98.32 27.33 26.9 1.43 479436 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella parvula 27.33 4.6 0.17 0.76
Shigella NR_104826.1 1530 253 1491 97.45 244.17 31.0 1.69 624 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Shigella sonnei 244.17 39.66 0.16 6.44
Shigella NR_104901.1 1515 46 1484 97.95 43.78 31.8 10.9 621 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Shigella boydii 43.78 6.49 0.15 1.17
Limosilactobacillus NR_104927.1 1502 79 1502 100.0 77.46 32.0 14.0 1613 Bacteria Bacillati Bacillota Bacilli Lactobacillales Lactobacillaceae Limosilactobacillus fermentum 77.46 1.43 0.02 2.01
Bacteroides NR_112936.1 1490 46 1490 100.0 45.28 31.1 5.67 817 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteroidaceae Bacteroides fragilis 45.28 1.08 0.02 1.17
Veillonella NR_113031.1 1524 408 1524 100.0 400.73 30.7 3.04 29466 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella parvula 400.73 11.62 0.03 10.39
Prevotella NR_113099.1 1479 59 1479 100.0 57.98 31.4 59.5 28128 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Prevotellaceae Prevotella corporis 57.98 1.17 0.02 1.5
Clostridioides NR_113132.1 1464 231 1464 100.0 227.25 30.1 59.7 1121308 Bacteria Bacillati Bacillota Clostridia Peptostreptococcales Peptostreptococcaceae Clostridioides difficile 227.25 4.09 0.02 5.88
Limosilactobacillus NR_113335.1 1501 13 1501 100.0 12.39 30.5 5.46 1613 Bacteria Bacillati Bacillota Bacilli Lactobacillales Lactobacillaceae Limosilactobacillus fermentum 12.39 0.85 0.07 0.33
Fusobacterium NR_113378.1 1480 64 1480 100.0 62.69 30.6 25.7 76859 Bacteria Fusobacteriati Fusobacteriota Fusobacteriia Fusobacteriales Fusobacteriaceae Fusobacterium animalis 62.69 1.33 0.02 1.63
Veillonella NR_113570.1 1520 17 1505 99.01 16.11 30.2 10.1 1110546 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella tobetsuensis 16.11 1.96 0.12 0.43
Escherichia NR_114042.1 1467 4 1467 100.0 3.72 29.7 0.75 562 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia coli 3.72 0.5 0.13 0.1
Escherichia NR_114079.1 1467 1 1261 85.96 0.86 27.4 1.0 564 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia fergusonii 0.86 0.35 0.4 0.03
Veillonella NR_115355.1 1498 444 1498 100.0 437.73 31.5 6.87 39778 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella dispar 437.73 13.11 0.03 11.31
Fusobacterium NR_117291.1 1441 13 1441 100.0 12.9 33.4 16.5 997347 Bacteria Fusobacteriati Fusobacteriota Fusobacteriia Fusobacteriales Fusobacteriaceae Fusobacterium animalis 12.9 0.41 0.03 0.33
Bacteroides NR_119164.1 1436 19 1436 100.0 18.68 31.7 7.68 817 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteroidaceae Bacteroides fragilis 18.68 0.67 0.04 0.48
Veillonella NR_119168.1 1513 2 1085 71.71 1.25 31.2 1.0 479436 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella parvula 1.25 0.87 0.69 0.05
Veillonella NR_119169.1 1513 2 1106 73.1 1.43 28.6 1.0 39778 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella dispar 1.43 0.89 0.62 0.05
Escherichia NR_136472.1 1504 56 1504 100.0 53.81 30.4 6.7 1499973 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia marmotae 53.81 2.02 0.04 1.43
Faecalibacterium NR_178280.1 1466 500 1465 99.93 489.59 31.0 15.7 411483 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium duncaniae 489.59 27.32 0.06 12.73
Paraburkholderia NR_178798.1 1428 1 1422 99.58 1.0 34.5 12.0 1441714 Bacteria Pseudomonadati Pseudomonadota Betaproteobacteria Burkholderiales Burkholderiaceae Paraburkholderia fungorum 1.0 0.06 0.06 0.03
Faecalibacterium NR_178971.1 1381 198 1381 100.0 194.33 31.4 10.3 1851427 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium butyricigenerans 194.33 14.21 0.07 5.04
Faecalibacterium NR_178972.1 1372 4 1369 99.78 3.39 31.5 2.75 1851428 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium longum 3.39 0.79 0.23 0.1
Veillonella NR_179325.1 1469 16 1465 99.73 15.58 30.6 3.38 2682456 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella nakazawae 15.58 1.23 0.08 0.41
Fusobacterium NR_179326.1 1400 1 1117 79.79 0.8 30.5 34.0 2686067 Bacteria Fusobacteriati Fusobacteriota Fusobacteriia Fusobacteriales Fusobacteriaceae Fusobacterium watanabei 0.8 0.4 0.5 0.03
Faecalibacterium NR_179388.1 1472 195 1469 99.8 191.24 30.8 21.2 2935520 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium hattorii 191.24 10.6 0.06 4.97

Only taxa present in the abundance table above the abundance_threshold parameter appear in the table.

genus reference ref length number of reads covbases % coverage mean depth mean baseq mean MAPQ taxid superkingdom kingdom phylum class order family species mean sd depth CV % reads
Escherichia NR_024570.1 1450 1 1404 96.83 0.97 34.3 13.0 562 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia coli 0.97 0.18 0.18 0.03
Escherichia NR_025569.1 1494 1 796 53.28 0.53 20.8 0.0 208962 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia albertii 0.53 0.5 0.94 0.03
Shigella NR_026331.1 1488 251 1488 100.0 246.32 29.7 7.99 623 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Shigella flexneri 246.32 6.17 0.03 6.41
Shigella NR_026332.1 1487 52 1487 100.0 51.27 30.3 45.9 622 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Shigella dysenteriae 51.27 1.21 0.02 1.33
Escherichia NR_027549.1 1473 21 1473 100.0 20.44 29.0 5.14 585054 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia fergusonii 20.44 1.66 0.08 0.54
Faecalibacterium NR_028961.1 1462 4 1456 99.59 3.24 29.9 1.75 853 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium prausnitzii 3.24 1.06 0.33 0.1
Veillonella NR_041879.1 1375 1 995 72.36 0.72 32.8 1.0 39778 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella dispar 0.72 0.45 0.62 0.03
Roseburia NR_042008.1 1485 56 1480 99.66 54.56 31.2 4.57 585394 Bacteria Bacillati Bacillota Clostridia Lachnospirales Lachnospiraceae Roseburia hominis 54.56 3.54 0.06 1.43
Akkermansia NR_042817.1 1433 4 1433 100.0 3.95 32.1 25.8 349741 Bacteria Pseudomonadati Verrucomicrobiota Verrucomicrobiia Verrucomicrobiales Akkermansiaceae Akkermansia muciniphila 3.95 0.24 0.06 0.1
Veillonella NR_043332.1 1497 81 1494 99.8 79.37 31.0 2.75 479436 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella parvula 79.37 4.54 0.06 2.07
Veillonella NR_044091.1 1344 155 1344 100.0 151.32 30.6 42.4 423477 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella rogosae 151.32 3.34 0.02 3.96
Akkermansia NR_074436.1 1505 11 1474 97.94 10.66 32.5 26.9 239935 Bacteria Pseudomonadati Verrucomicrobiota Verrucomicrobiia Verrucomicrobiales Akkermansiaceae Akkermansia muciniphila 10.66 1.59 0.15 0.28
Bacteroides NR_074784.2 1529 5 1490 97.45 4.23 30.3 3.0 272559 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteroidaceae Bacteroides fragilis 4.23 1.08 0.25 0.13
Roseburia NR_074809.1 1535 106 1495 97.39 101.67 30.5 18.8 585394 Bacteria Bacillati Bacillota Clostridia Lachnospirales Lachnospiraceae Roseburia hominis 101.67 16.8 0.17 2.71
Escherichia NR_074902.1 1542 386 1518 98.44 368.75 30.3 7.65 585054 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia fergusonii 368.75 58.98 0.16 9.86
Salmonella NR_074910.1 1544 4 1501 97.22 3.85 29.5 4.75 90371 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Salmonella enterica 3.85 0.69 0.18 0.1
Veillonella NR_074980.1 1551 36 1520 98.0 33.53 28.2 1.22 479436 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella parvula 33.53 5.5 0.16 0.92
Shigella NR_104826.1 1530 200 1492 97.52 192.59 30.8 1.65 624 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Shigella sonnei 192.59 31.27 0.16 5.11
Shigella NR_104901.1 1515 31 1484 97.95 29.89 31.4 12.7 621 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Shigella boydii 29.89 4.41 0.15 0.79
Limosilactobacillus NR_104927.1 1502 82 1502 100.0 81.29 31.8 13.8 1613 Bacteria Bacillati Bacillota Bacilli Lactobacillales Lactobacillaceae Limosilactobacillus fermentum 81.29 1.26 0.02 2.1
Bacteroides NR_112936.1 1490 42 1490 100.0 41.03 30.5 5.19 817 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteroidaceae Bacteroides fragilis 41.03 1.0 0.02 1.07
Veillonella NR_113031.1 1524 565 1524 100.0 551.96 30.7 3.1 29466 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella parvula 551.96 15.9 0.03 14.44
Prevotella NR_113099.1 1479 73 1479 100.0 72.22 30.4 59.9 28128 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Prevotellaceae Prevotella corporis 72.22 1.33 0.02 1.87
Clostridioides NR_113132.1 1464 230 1464 100.0 224.85 30.2 59.5 1121308 Bacteria Bacillati Bacillota Clostridia Peptostreptococcales Peptostreptococcaceae Clostridioides difficile 224.85 4.63 0.02 5.88
Limosilactobacillus NR_113335.1 1501 14 1501 100.0 13.74 28.2 3.21 1613 Bacteria Bacillati Bacillota Bacilli Lactobacillales Lactobacillaceae Limosilactobacillus fermentum 13.74 0.62 0.05 0.36
Fusobacterium NR_113378.1 1480 91 1480 100.0 89.75 30.5 22.9 76859 Bacteria Fusobacteriati Fusobacteriota Fusobacteriia Fusobacteriales Fusobacteriaceae Fusobacterium animalis 89.75 1.52 0.02 2.33
Veillonella NR_113570.1 1520 22 1506 99.08 19.62 30.4 10.7 1110546 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella tobetsuensis 19.62 3.01 0.15 0.56
Escherichia NR_114042.1 1467 8 1462 99.66 7.82 28.0 1.38 562 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia coli 7.82 0.69 0.09 0.2
Escherichia NR_114079.1 1467 2 1157 78.87 1.41 32.1 4.0 564 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia fergusonii 1.41 0.82 0.58 0.05
Veillonella NR_115355.1 1498 580 1498 100.0 570.36 31.1 7.58 39778 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella dispar 570.36 17.67 0.03 14.82
Fusobacterium NR_117291.1 1441 20 1441 100.0 19.8 30.7 10.7 997347 Bacteria Fusobacteriati Fusobacteriota Fusobacteriia Fusobacteriales Fusobacteriaceae Fusobacterium animalis 19.8 0.54 0.03 0.51
Veillonella NR_117759.1 1345 3 1343 99.85 2.94 27.8 20.7 479436 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella parvula 2.94 0.27 0.09 0.08
Bacteroides NR_119164.1 1436 11 1436 100.0 10.91 31.4 15.2 817 Bacteria Pseudomonadati Bacteroidota Bacteroidia Bacteroidales Bacteroidaceae Bacteroides fragilis 10.91 0.34 0.03 0.28
Veillonella NR_119168.1 1513 3 1040 68.74 1.87 31.1 6.33 479436 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella parvula 1.87 1.35 0.72 0.08
Veillonella NR_119169.1 1513 2 1101 72.77 1.42 32.5 1.0 39778 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella dispar 1.42 0.89 0.62 0.05
Escherichia NR_136472.1 1504 53 1504 100.0 52.1 29.6 4.06 1499973 Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia marmotae 52.1 1.5 0.03 1.35
Faecalibacterium NR_178280.1 1466 347 1465 99.93 340.01 30.7 16.4 411483 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium duncaniae 340.01 18.79 0.06 8.87
Faecalibacterium NR_178971.1 1381 142 1378 99.78 139.55 31.6 11.0 1851427 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium butyricigenerans 139.55 9.96 0.07 3.63
Faecalibacterium NR_178972.1 1372 1 1342 97.81 0.98 31.5 1.0 1851428 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium longum 0.98 0.15 0.15 0.03
Veillonella NR_179325.1 1469 22 1465 99.73 21.48 29.7 5.95 2682456 Bacteria Bacillati Bacillota Negativicutes Veillonellales Veillonellaceae Veillonella nakazawae 21.48 1.57 0.07 0.56
Fusobacterium NR_179326.1 1400 1 1397 99.79 1.0 35.6 1.0 2686067 Bacteria Fusobacteriati Fusobacteriota Fusobacteriia Fusobacteriales Fusobacteriaceae Fusobacterium watanabei 1.0 0.05 0.05 0.03
Faecalibacterium NR_179388.1 1472 191 1470 99.86 186.25 30.1 20.7 2935520 Bacteria Bacillati Bacillota Clostridia Eubacteriales Oscillospiraceae Faecalibacterium hattorii 186.25 10.65 0.06 4.88

Scatter plot showing, for each reference, the coverage (y-axis) and the number of mapped reads (x-axis). Hover the cursor over the points to show the reference name and species. Zoom into a specific region to distinguish between closest points.

Scatter plot showing, for each reference, the coverage (y-axis) and the number of mapped reads (x-axis). Hover the cursor over the points to show the reference name and species. Zoom into a specific region to distinguish between closest points.

Scatter plot showing, for each reference, the coverage (y-axis) and the number of mapped reads (x-axis). Hover the cursor over the points to show the reference name and species. Zoom into a specific region to distinguish between closest points.

To illustrate consistency of coverage between the reference sequences, each reference is divided into 100 evenly sized windows, and the average depth across all positions in the window is plotted in a cell in the heatmap. Only references with at least an averagesequencing depth > 1 across the entire reference sequence are included in the heatmap.

To illustrate consistency of coverage between the reference sequences, each reference is divided into 100 evenly sized windows, and the average depth across all positions in the window is plotted in a cell in the heatmap. Only references with at least an averagesequencing depth > 1 across the entire reference sequence are included in the heatmap.

To illustrate consistency of coverage between the reference sequences, each reference is divided into 100 evenly sized windows, and the average depth across all positions in the window is plotted in a cell in the heatmap. Only references with at least an averagesequencing depth > 1 across the entire reference sequence are included in the heatmap.

Software versions

Name Version
pysam 0.23.0
pandas 2.2.3
fastcat 0.20.0
minimap2 2.28-r1209
samtools 1.21
taxonkit v0.19.0
Kraken 2.1.3

Workflow parameters

Key Value
fastq wf-16s/data/wf-16s-demo/test_data/
bam None
sample None
sample_sheet None
classifier minimap2
exclude_host None
max_len 2000
min_len 800
min_read_qual None
threads 4
server_threads 2
kraken_clients 2
taxonomy None
reference None
ref2taxid None
database None
taxonomic_rank G
minimap2filter None
minimap2exclude False
keep_bam False
minimap2_by_reference True
min_percent_identity 95
min_ref_coverage 90
store_dir wf-16s/store_dir
out_dir wf-16s
include_read_assignments False
igv False
output_unclassified False
bracken_length None
bracken_threshold 10
port 8080
host localhost
external_kraken2 False
kraken2_memory_mapping False
kraken2_confidence 0
batch_size 0
real_time False
read_limit None
database_set ncbi_16s_18s
database_sets {'ncbi_16s_18s': {'reference': 'https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_16s_18s.fna', 'database': 'https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_kraken2.tar.gz', 'ref2taxid': 'https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ref2taxid.targloci.tsv', 'taxonomy': 'https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2025-01-01.zip'}, 'ncbi_16s_18s_28s_ITS': {'reference': 'https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS.fna', 'database': 'https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS_kraken2.tar.gz', 'ref2taxid': 'https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ref2taxid.ncbi_16s_18s_28s_ITS.tsv', 'taxonomy': 'https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2025-01-01.zip'}, 'SILVA_138_1': {'database': None}}
abundance_threshold 1
n_taxa_barplot 9
amr False
amr_db resfinder
amr_minid 80
amr_mincov 80
analyse_unclassified False