wf-16s Sequencing Report

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

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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	2349	2493	9684	Bacteria	Bacteria_none	Bacteria;Bacteria_none;Bacillota
Bacteroidota	279	121	125	525	Bacteria	Bacteria_none	Bacteria;Bacteria_none;Bacteroidota
Fusobacteriota	206	73	109	388	Bacteria	Bacteria_none	Bacteria;Bacteria_none;Fusobacteriota
Pseudomonadota	2116	1187	979	4282	Bacteria	Bacteria_none	Bacteria;Bacteria_none;Pseudomonadota
Verrucomicrobiota	19	1	15	35	Bacteria	Bacteria_none	Bacteria;Bacteria_none;Verrucomicrobiota
Unknown	376	196	192	764	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	86	94	322	Bacteria	Bacteria_none	Bacillota	Bacteria;Bacteria_none;Bacillota;Bacilli
Clostridia	2324	1216	1016	4556	Bacteria	Bacteria_none	Bacillota	Bacteria;Bacteria_none;Bacillota;Clostridia
Negativicutes	2376	1047	1383	4806	Bacteria	Bacteria_none	Bacillota	Bacteria;Bacteria_none;Bacillota;Negativicutes
Bacteroidia	279	121	125	525	Bacteria	Bacteria_none	Bacteroidota	Bacteria;Bacteria_none;Bacteroidota;Bacteroidia
Fusobacteriia	206	73	109	388	Bacteria	Bacteria_none	Fusobacteriota	Bacteria;Bacteria_none;Fusobacteriota;Fusobacteriia
Betaproteobacteria	1	1	0	2	Bacteria	Bacteria_none	Pseudomonadota	Bacteria;Bacteria_none;Pseudomonadota;Betaproteobacteria
Gammaproteobacteria	2115	1186	979	4280	Bacteria	Bacteria_none	Pseudomonadota	Bacteria;Bacteria_none;Pseudomonadota;Gammaproteobacteria
Verrucomicrobiia	19	1	15	35	Bacteria	Bacteria_none	Verrucomicrobiota	Bacteria;Bacteria_none;Verrucomicrobiota;Verrucomicrobiia
Unknown	376	196	192	764	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	86	94	322	Bacteria	Bacteria_none	Bacillota	Bacilli	Bacteria;Bacteria_none;Bacillota;Bacilli;Lactobacillales
Eubacteriales	1441	853	644	2938	Bacteria	Bacteria_none	Bacillota	Clostridia	Bacteria;Bacteria_none;Bacillota;Clostridia;Eubacteriales
Lachnospirales	376	139	157	672	Bacteria	Bacteria_none	Bacillota	Clostridia	Bacteria;Bacteria_none;Bacillota;Clostridia;Lachnospirales
Peptostreptococcales	507	224	215	946	Bacteria	Bacteria_none	Bacillota	Clostridia	Bacteria;Bacteria_none;Bacillota;Clostridia;Peptostreptococcales
Veillonellales	2376	1047	1383	4806	Bacteria	Bacteria_none	Bacillota	Negativicutes	Bacteria;Bacteria_none;Bacillota;Negativicutes;Veillonellales
Bacteroidales	279	121	125	525	Bacteria	Bacteria_none	Bacteroidota	Bacteroidia	Bacteria;Bacteria_none;Bacteroidota;Bacteroidia;Bacteroidales
Fusobacteriales	206	73	109	388	Bacteria	Bacteria_none	Fusobacteriota	Fusobacteriia	Bacteria;Bacteria_none;Fusobacteriota;Fusobacteriia;Fusobacteriales
Burkholderiales	1	1	0	2	Bacteria	Bacteria_none	Pseudomonadota	Betaproteobacteria	Bacteria;Bacteria_none;Pseudomonadota;Betaproteobacteria;Burkholderiales
Enterobacterales	2115	1186	978	4279	Bacteria	Bacteria_none	Pseudomonadota	Gammaproteobacteria	Bacteria;Bacteria_none;Pseudomonadota;Gammaproteobacteria;Enterobacterales
Verrucomicrobiales	19	1	15	35	Bacteria	Bacteria_none	Verrucomicrobiota	Verrucomicrobiia	Bacteria;Bacteria_none;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales
Unknown	376	196	192	764	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	86	94	322	Bacteria	Bacteria_none	Bacillota	Bacilli	Lactobacillales	Bacteria;Bacteria_none;Bacillota;Bacilli;Lactobacillales;Lactobacillaceae
Oscillospiraceae	1441	853	644	2938	Bacteria	Bacteria_none	Bacillota	Clostridia	Eubacteriales	Bacteria;Bacteria_none;Bacillota;Clostridia;Eubacteriales;Oscillospiraceae
Lachnospiraceae	376	139	157	672	Bacteria	Bacteria_none	Bacillota	Clostridia	Lachnospirales	Bacteria;Bacteria_none;Bacillota;Clostridia;Lachnospirales;Lachnospiraceae
Peptostreptococcaceae	507	224	215	946	Bacteria	Bacteria_none	Bacillota	Clostridia	Peptostreptococcales	Bacteria;Bacteria_none;Bacillota;Clostridia;Peptostreptococcales;Peptostreptococcaceae
Veillonellaceae	2376	1047	1383	4806	Bacteria	Bacteria_none	Bacillota	Negativicutes	Veillonellales	Bacteria;Bacteria_none;Bacillota;Negativicutes;Veillonellales;Veillonellaceae
Bacteroidaceae	157	64	53	274	Bacteria	Bacteria_none	Bacteroidota	Bacteroidia	Bacteroidales	Bacteria;Bacteria_none;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae
Prevotellaceae	122	57	72	251	Bacteria	Bacteria_none	Bacteroidota	Bacteroidia	Bacteroidales	Bacteria;Bacteria_none;Bacteroidota;Bacteroidia;Bacteroidales;Prevotellaceae
Fusobacteriaceae	206	73	109	388	Bacteria	Bacteria_none	Fusobacteriota	Fusobacteriia	Fusobacteriales	Bacteria;Bacteria_none;Fusobacteriota;Fusobacteriia;Fusobacteriales;Fusobacteriaceae
Burkholderiaceae	1	1	0	2	Bacteria	Bacteria_none	Pseudomonadota	Betaproteobacteria	Burkholderiales	Bacteria;Bacteria_none;Pseudomonadota;Betaproteobacteria;Burkholderiales;Burkholderiaceae
Enterobacteriaceae	2115	1186	978	4279	Bacteria	Bacteria_none	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Bacteria;Bacteria_none;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae
Akkermansiaceae	19	1	15	35	Bacteria	Bacteria_none	Verrucomicrobiota	Verrucomicrobiia	Verrucomicrobiales	Bacteria;Bacteria_none;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales;Akkermansiaceae
Unknown	376	196	192	764	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	86	94	322	Bacteria	Bacteria_none	Bacillota	Bacilli	Lactobacillales	Lactobacillaceae	Bacteria;Bacteria_none;Bacillota;Bacilli;Lactobacillales;Lactobacillaceae;Limosilactobacillus
Faecalibacterium	1441	853	644	2938	Bacteria	Bacteria_none	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Bacteria;Bacteria_none;Bacillota;Clostridia;Eubacteriales;Oscillospiraceae;Faecalibacterium
Roseburia	376	139	157	672	Bacteria	Bacteria_none	Bacillota	Clostridia	Lachnospirales	Lachnospiraceae	Bacteria;Bacteria_none;Bacillota;Clostridia;Lachnospirales;Lachnospiraceae;Roseburia
Clostridioides	507	224	215	946	Bacteria	Bacteria_none	Bacillota	Clostridia	Peptostreptococcales	Peptostreptococcaceae	Bacteria;Bacteria_none;Bacillota;Clostridia;Peptostreptococcales;Peptostreptococcaceae;Clostridioides
Veillonella	2376	1047	1383	4806	Bacteria	Bacteria_none	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Bacteria;Bacteria_none;Bacillota;Negativicutes;Veillonellales;Veillonellaceae;Veillonella
Bacteroides	157	64	53	274	Bacteria	Bacteria_none	Bacteroidota	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteria;Bacteria_none;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides
Prevotella	122	57	72	251	Bacteria	Bacteria_none	Bacteroidota	Bacteroidia	Bacteroidales	Prevotellaceae	Bacteria;Bacteria_none;Bacteroidota;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella
Fusobacterium	206	73	109	388	Bacteria	Bacteria_none	Fusobacteriota	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Bacteria;Bacteria_none;Fusobacteriota;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium
Paraburkholderia	1	1	0	2	Bacteria	Bacteria_none	Pseudomonadota	Betaproteobacteria	Burkholderiales	Burkholderiaceae	Bacteria;Bacteria_none;Pseudomonadota;Betaproteobacteria;Burkholderiales;Burkholderiaceae;Paraburkholderia
Escherichia	937	531	452	1920	Bacteria	Bacteria_none	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Bacteria;Bacteria_none;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia
Salmonella	1	0	4	5	Bacteria	Bacteria_none	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Bacteria;Bacteria_none;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Salmonella
Shigella	1177	655	522	2354	Bacteria	Bacteria_none	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Bacteria;Bacteria_none;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Shigella
Akkermansia	19	1	15	35	Bacteria	Bacteria_none	Verrucomicrobiota	Verrucomicrobiia	Verrucomicrobiales	Akkermansiaceae	Bacteria;Bacteria_none;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales;Akkermansiaceae;Akkermansia
Unknown	376	196	192	764	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	2313	2210	2361	2351	Bacteria	Bacteria_none	Bacteria;Bacteria_none;Bacillota
Bacteroidota	140	115	122	116	Bacteria	Bacteria_none	Bacteria;Bacteria_none;Bacteroidota
Fusobacteriota	99	69	105	99	Bacteria	Bacteria_none	Bacteria;Bacteria_none;Fusobacteriota
Pseudomonadota	969	1137	932	965	Bacteria	Bacteria_none	Bacteria;Bacteria_none;Pseudomonadota
Verrucomicrobiota	11	1	15	10	Bacteria	Bacteria_none	Bacteria;Bacteria_none;Verrucomicrobiota
Unknown	185	185	182	176	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	80	87	85	Bacteria	Bacteria_none	Bacillota	Bacteria;Bacteria_none;Bacillota;Bacilli
Clostridia	1118	1162	962	1093	Bacteria	Bacteria_none	Bacillota	Bacteria;Bacteria_none;Bacillota;Clostridia
Negativicutes	1140	988	1322	1095	Bacteria	Bacteria_none	Bacillota	Bacteria;Bacteria_none;Bacillota;Negativicutes
Bacteroidia	139	111	116	123	Bacteria	Bacteria_none	Bacteroidota	Bacteria;Bacteria_none;Bacteroidota;Bacteroidia
Fusobacteriia	90	70	105	88	Bacteria	Bacteria_none	Fusobacteriota	Bacteria;Bacteria_none;Fusobacteriota;Fusobacteriia
Betaproteobacteria	1	1	0	1	Bacteria	Bacteria_none	Pseudomonadota	Bacteria;Bacteria_none;Pseudomonadota;Betaproteobacteria
Gammaproteobacteria	984	1119	926	1046	Bacteria	Bacteria_none	Pseudomonadota	Bacteria;Bacteria_none;Pseudomonadota;Gammaproteobacteria
Verrucomicrobiia	12	1	15	10	Bacteria	Bacteria_none	Verrucomicrobiota	Bacteria;Bacteria_none;Verrucomicrobiota;Verrucomicrobiia
Unknown	169	185	184	176	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	72	80	91	72	Bacteria	Bacteria_none	Bacillota	Bacilli	Bacteria;Bacteria_none;Bacillota;Bacilli;Lactobacillales
Eubacteriales	672	802	610	672	Bacteria	Bacteria_none	Bacillota	Clostridia	Bacteria;Bacteria_none;Bacillota;Clostridia;Eubacteriales
Lachnospirales	179	134	147	164	Bacteria	Bacteria_none	Bacillota	Clostridia	Bacteria;Bacteria_none;Bacillota;Clostridia;Lachnospirales
Peptostreptococcales	245	209	205	222	Bacteria	Bacteria_none	Bacillota	Clostridia	Bacteria;Bacteria_none;Bacillota;Clostridia;Peptostreptococcales
Veillonellales	1135	977	1322	1177	Bacteria	Bacteria_none	Bacillota	Negativicutes	Bacteria;Bacteria_none;Bacillota;Negativicutes;Veillonellales
Bacteroidales	121	118	119	132	Bacteria	Bacteria_none	Bacteroidota	Bacteroidia	Bacteria;Bacteria_none;Bacteroidota;Bacteroidia;Bacteroidales
Fusobacteriales	107	72	104	82	Bacteria	Bacteria_none	Fusobacteriota	Fusobacteriia	Bacteria;Bacteria_none;Fusobacteriota;Fusobacteriia;Fusobacteriales
Burkholderiales	0	1	0	0	Bacteria	Bacteria_none	Pseudomonadota	Betaproteobacteria	Bacteria;Bacteria_none;Pseudomonadota;Betaproteobacteria;Burkholderiales
Enterobacterales	986	1142	925	991	Bacteria	Bacteria_none	Pseudomonadota	Gammaproteobacteria	Bacteria;Bacteria_none;Pseudomonadota;Gammaproteobacteria;Enterobacterales
Verrucomicrobiales	11	1	13	9	Bacteria	Bacteria_none	Verrucomicrobiota	Verrucomicrobiia	Bacteria;Bacteria_none;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales
Unknown	188	180	180	195	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	71	79	91	79	Bacteria	Bacteria_none	Bacillota	Bacilli	Lactobacillales	Bacteria;Bacteria_none;Bacillota;Bacilli;Lactobacillales;Lactobacillaceae
Oscillospiraceae	691	805	609	715	Bacteria	Bacteria_none	Bacillota	Clostridia	Eubacteriales	Bacteria;Bacteria_none;Bacillota;Clostridia;Eubacteriales;Oscillospiraceae
Lachnospiraceae	181	130	148	168	Bacteria	Bacteria_none	Bacillota	Clostridia	Lachnospirales	Bacteria;Bacteria_none;Bacillota;Clostridia;Lachnospirales;Lachnospiraceae
Peptostreptococcaceae	253	209	205	231	Bacteria	Bacteria_none	Bacillota	Clostridia	Peptostreptococcales	Bacteria;Bacteria_none;Bacillota;Clostridia;Peptostreptococcales;Peptostreptococcaceae
Veillonellaceae	1103	1002	1318	1132	Bacteria	Bacteria_none	Bacillota	Negativicutes	Veillonellales	Bacteria;Bacteria_none;Bacillota;Negativicutes;Veillonellales;Veillonellaceae
Bacteroidaceae	77	61	53	61	Bacteria	Bacteria_none	Bacteroidota	Bacteroidia	Bacteroidales	Bacteria;Bacteria_none;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae
Prevotellaceae	52	55	66	60	Bacteria	Bacteria_none	Bacteroidota	Bacteroidia	Bacteroidales	Bacteria;Bacteria_none;Bacteroidota;Bacteroidia;Bacteroidales;Prevotellaceae
Fusobacteriaceae	97	70	103	102	Bacteria	Bacteria_none	Fusobacteriota	Fusobacteriia	Fusobacteriales	Bacteria;Bacteria_none;Fusobacteriota;Fusobacteriia;Fusobacteriales;Fusobacteriaceae
Burkholderiaceae	1	1	0	0	Bacteria	Bacteria_none	Pseudomonadota	Betaproteobacteria	Burkholderiales	Bacteria;Bacteria_none;Pseudomonadota;Betaproteobacteria;Burkholderiales;Burkholderiaceae
Enterobacteriaceae	1004	1120	929	978	Bacteria	Bacteria_none	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Bacteria;Bacteria_none;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae
Akkermansiaceae	6	1	12	5	Bacteria	Bacteria_none	Verrucomicrobiota	Verrucomicrobiia	Verrucomicrobiales	Bacteria;Bacteria_none;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales;Akkermansiaceae
Unknown	180	183	182	185	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	66	75	93	82	Bacteria	Bacteria_none	Bacillota	Bacilli	Lactobacillales	Lactobacillaceae	Bacteria;Bacteria_none;Bacillota;Bacilli;Lactobacillales;Lactobacillaceae;Limosilactobacillus
Faecalibacterium	712	807	608	710	Bacteria	Bacteria_none	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Bacteria;Bacteria_none;Bacillota;Clostridia;Eubacteriales;Oscillospiraceae;Faecalibacterium
Roseburia	175	130	149	145	Bacteria	Bacteria_none	Bacillota	Clostridia	Lachnospirales	Lachnospiraceae	Bacteria;Bacteria_none;Bacillota;Clostridia;Lachnospirales;Lachnospiraceae;Roseburia
Clostridioides	237	216	202	211	Bacteria	Bacteria_none	Bacillota	Clostridia	Peptostreptococcales	Peptostreptococcaceae	Bacteria;Bacteria_none;Bacillota;Clostridia;Peptostreptococcales;Peptostreptococcaceae;Clostridioides
Veillonella	1117	995	1325	1134	Bacteria	Bacteria_none	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Bacteria;Bacteria_none;Bacillota;Negativicutes;Veillonellales;Veillonellaceae;Veillonella
Bacteroides	82	59	50	75	Bacteria	Bacteria_none	Bacteroidota	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteria;Bacteria_none;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides
Prevotella	57	53	65	65	Bacteria	Bacteria_none	Bacteroidota	Bacteroidia	Bacteroidales	Prevotellaceae	Bacteria;Bacteria_none;Bacteroidota;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella
Fusobacterium	86	67	102	87	Bacteria	Bacteria_none	Fusobacteriota	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Bacteria;Bacteria_none;Fusobacteriota;Fusobacteriia;Fusobacteriales;Fusobacteriaceae;Fusobacterium
Paraburkholderia	1	1	0	1	Bacteria	Bacteria_none	Pseudomonadota	Betaproteobacteria	Burkholderiales	Burkholderiaceae	Bacteria;Bacteria_none;Pseudomonadota;Betaproteobacteria;Burkholderiales;Burkholderiaceae;Paraburkholderia
Escherichia	442	507	424	454	Bacteria	Bacteria_none	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Bacteria;Bacteria_none;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia
Salmonella	0	0	4	0	Bacteria	Bacteria_none	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Bacteria;Bacteria_none;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Salmonella
Shigella	549	618	502	547	Bacteria	Bacteria_none	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Bacteria;Bacteria_none;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Shigella
Akkermansia	6	1	13	10	Bacteria	Bacteria_none	Verrucomicrobiota	Verrucomicrobiia	Verrucomicrobiales	Akkermansiaceae	Bacteria;Bacteria_none;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales;Akkermansiaceae;Akkermansia
Unknown	186	187	179	195	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.

index	reference	startpos	ref length	number of reads	covbases	pc coverage	meandepth	meanbaseq	meanmapq	taxid	superkingdom	kingdom	phylum	class	order	family	genus	species	mean	sd	Coefficient of Variance	pcreads
0	NR_024570.1	1	1450	1	1424	98.2069	0.982069	32.0	1.0	562	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia coli	0.98	0.13	0.13	0.01
1	NR_025569.1	1	1494	1	1446	96.7871	0.967871	25.1	1.0	208962	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia albertii	0.97	0.18	0.19	0.01
2	NR_026331.1	1	1488	537	1488	100.0	526.392	30.3	8.62	623	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Shigella	Shigella flexneri	526.39	14.18	0.03	6.85
3	NR_026332.1	1	1487	144	1487	100.0	141.111	30.6	47.3	622	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Shigella	Shigella dysenteriae	141.11	2.74	0.02	1.84
4	NR_027549.1	1	1473	55	1473	100.0	52.5492	29.9	6.89	585054	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia fergusonii	52.55	4.86	0.09	0.7
5	NR_028961.1	1	1462	34	1462	100.0	29.4166	29.9	5.26	853	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	Faecalibacterium prausnitzii	29.42	5.05	0.17	0.43
6	NR_041879.1	1	1375	2	1357	98.6909	1.76436	28.8	19.5	39778	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella dispar	1.76	0.45	0.26	0.03
7	NR_042008.1	1	1485	153	1483	99.8653	150.098	30.9	4.48	585394	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Lachnospirales	Lachnospiraceae	Roseburia	Roseburia hominis	150.1	9.29	0.06	1.95
8	NR_042817.1	1	1433	2	1433	100.0	1.97348	32.4	1.0	349741	Bacteria	unclassified Bacteria kingdom	Verrucomicrobiota	Verrucomicrobiia	Verrucomicrobiales	Akkermansiaceae	Akkermansia	Akkermansia muciniphila	1.97	0.16	0.08	0.03
9	NR_043332.1	1	1497	121	1494	99.7996	118.653	30.3	2.99	479436	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella parvula	118.65	6.77	0.06	1.54
10	NR_044091.1	1	1344	251	1344	100.0	246.15	30.6	43.8	423477	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella rogosae	246.15	4.53	0.02	3.2
11	NR_074436.1	1	1505	17	1474	97.9402	16.4718	31.1	23.8	239935	Bacteria	unclassified Bacteria kingdom	Verrucomicrobiota	Verrucomicrobiia	Verrucomicrobiales	Akkermansiaceae	Akkermansia	Akkermansia muciniphila	16.47	2.44	0.15	0.22
12	NR_074784.2	1	1529	6	1484	97.0569	5.6743	24.2	1.0	272559	Bacteria	unclassified Bacteria kingdom	Bacteroidota	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	Bacteroides fragilis	5.67	1.08	0.19	0.08
13	NR_074809.1	1	1535	238	1496	97.4593	227.607	30.0	18.4	585394	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Lachnospirales	Lachnospiraceae	Roseburia	Roseburia hominis	227.61	37.34	0.16	3.04
14	NR_074902.1	1	1542	790	1508	97.7951	753.079	30.4	6.93	585054	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia fergusonii	753.08	120.39	0.16	10.08
15	NR_074910.1	1	1544	1	1492	96.6321	0.966321	34.5	1.0	90371	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Salmonella	Salmonella enterica	0.97	0.18	0.19	0.01
16	NR_074980.1	1	1551	77	1525	98.3237	71.5016	26.7	1.25	479436	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella parvula	71.5	11.69	0.16	0.98
17	NR_104826.1	1	1530	450	1493	97.5817	433.352	30.9	1.47	624	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Shigella	Shigella sonnei	433.35	70.46	0.16	5.74
18	NR_104901.1	1	1515	89	1484	97.9538	85.0106	30.4	11.8	621	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Shigella	Shigella boydii	85.01	12.54	0.15	1.14
19	NR_104927.1	1	1502	129	1502	100.0	126.846	31.6	13.1	1613	Bacteria	unclassified Bacteria kingdom	Bacillota	Bacilli	Lactobacillales	Lactobacillaceae	Limosilactobacillus	Limosilactobacillus fermentum	126.85	2.16	0.02	1.65
21	NR_112172.1	1	1466	1	1108	75.5798	0.755798	31.7	14.0	1121308	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Peptostreptococcales	Peptostreptococcaceae	Clostridioides	Clostridioides difficile	0.76	0.43	0.57	0.01
22	NR_112558.1	1	1110	1	766	69.009	0.69009	27.2	20.0	562	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia coli	0.69	0.46	0.67	0.01
23	NR_112936.1	1	1490	121	1490	100.0	118.256	30.7	5.6	817	Bacteria	unclassified Bacteria kingdom	Bacteroidota	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	Bacteroides fragilis	118.26	2.94	0.02	1.54
24	NR_113031.1	1	1524	971	1524	100.0	954.584	30.5	3.15	29466	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella parvula	954.58	27.28	0.03	12.39
25	NR_113099.1	1	1479	132	1479	100.0	129.236	31.0	59.9	28128	Bacteria	unclassified Bacteria kingdom	Bacteroidota	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella	Prevotella corporis	129.24	2.76	0.02	1.68
26	NR_113132.1	1	1464	533	1464	100.0	521.255	30.3	59.7	1121308	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Peptostreptococcales	Peptostreptococcaceae	Clostridioides	Clostridioides difficile	521.26	9.48	0.02	6.8
27	NR_113335.1	1	1501	16	1501	100.0	15.6056	29.5	3.44	1613	Bacteria	unclassified Bacteria kingdom	Bacillota	Bacilli	Lactobacillales	Lactobacillaceae	Limosilactobacillus	Limosilactobacillus fermentum	15.61	0.89	0.06	0.2
28	NR_113378.1	1	1480	173	1480	100.0	170.228	30.4	25.7	76859	Bacteria	unclassified Bacteria kingdom	Fusobacteriota	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium	Fusobacterium animalis	170.23	2.97	0.02	2.21
29	NR_113570.1	1	1520	36	1506	99.0789	32.4493	30.6	8.19	1110546	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella tobetsuensis	32.45	4.4	0.14	0.46
30	NR_114042.1	1	1467	7	1467	100.0	6.77641	25.8	1.71	562	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia coli	6.78	0.6	0.09	0.09
31	NR_114079.1	1	1467	9	1467	100.0	7.92365	30.1	7.67	564	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia fergusonii	7.92	1.39	0.18	0.11
32	NR_115355.1	1	1498	993	1498	100.0	976.981	31.5	7.78	39778	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella dispar	976.98	29.46	0.03	12.67
33	NR_117291.1	1	1441	41	1441	100.0	40.0965	30.3	7.83	997347	Bacteria	unclassified Bacteria kingdom	Fusobacteriota	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium	Fusobacterium animalis	40.1	1.17	0.03	0.52
34	NR_117759.1	1	1345	1	1268	94.2751	0.942751	31.5	60.0	479436	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella parvula	0.94	0.23	0.24	0.01
35	NR_119164.1	1	1436	39	1436	100.0	38.4847	30.8	10.9	817	Bacteria	unclassified Bacteria kingdom	Bacteroidota	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	Bacteroides fragilis	38.48	1.21	0.03	0.5
36	NR_119168.1	1	1513	3	1078	71.2492	1.77726	27.5	2.33	479436	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella parvula	1.78	1.32	0.74	0.04
37	NR_119169.1	1	1513	3	1072	70.8526	1.92135	31.8	1.0	39778	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella dispar	1.92	1.3	0.68	0.04
38	NR_136472.1	1	1504	127	1504	100.0	125.36	31.2	5.76	1499973	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia marmotae	125.36	2.17	0.02	1.62
39	NR_163639.1	1	1532	2	1110	72.4543	1.41123	20.6	4.0	1911679	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella infantium	1.41	0.89	0.63	0.03
40	NR_178280.1	1	1466	757	1466	100.0	742.695	30.9	15.3	411483	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	Faecalibacterium duncaniae	742.7	41.24	0.06	9.66
41	NR_178798.1	1	1428	1	1410	98.7395	0.987395	26.3	3.0	1441714	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Betaproteobacteria	Burkholderiales	Burkholderiaceae	Paraburkholderia	Paraburkholderia fungorum	0.99	0.11	0.11	0.01
42	NR_178971.1	1	1381	320	1381	100.0	314.002	31.2	10.6	1851427	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	Faecalibacterium butyricigenerans	314.0	22.43	0.07	4.08
43	NR_178972.1	1	1372	12	1372	100.0	11.4956	28.8	1.42	1851428	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	Faecalibacterium longum	11.5	1.37	0.12	0.15
44	NR_179325.1	1	1469	37	1465	99.7277	35.6685	29.7	5.43	2682456	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella nakazawae	35.67	2.48	0.07	0.47
45	NR_179388.1	1	1472	403	1472	100.0	393.34	30.9	22.3	2935520	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	Faecalibacterium hattorii	393.34	21.89	0.06	5.14

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

index	reference	startpos	ref length	number of reads	covbases	pc coverage	meandepth	meanbaseq	meanmapq	taxid	superkingdom	kingdom	phylum	class	order	family	genus	species	mean	sd	Coefficient of Variance	pcreads
0	NR_025569.1	1	1494	2	1450	97.0549	1.44712	30.5	0.5	208962	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia albertii	1.45	0.55	0.38	0.05
1	NR_026331.1	1	1488	303	1488	100.0	297.751	30.7	9.17	623	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Shigella	Shigella flexneri	297.75	6.73	0.02	7.72
2	NR_026332.1	1	1487	66	1487	100.0	65.2703	30.9	48.1	622	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Shigella	Shigella dysenteriae	65.27	1.17	0.02	1.68
3	NR_027549.1	1	1473	30	1473	100.0	29.1677	30.6	8.17	585054	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia fergusonii	29.17	2.67	0.09	0.76
4	NR_028961.1	1	1462	18	1461	99.9316	15.3967	29.8	4.56	853	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	Faecalibacterium prausnitzii	15.4	3.44	0.22	0.46
5	NR_041879.1	1	1375	1	1049	76.2909	0.762909	33.5	12.0	39778	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella dispar	0.76	0.43	0.57	0.03
6	NR_042008.1	1	1485	58	1480	99.6633	57.2121	31.6	3.4	585394	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Lachnospirales	Lachnospiraceae	Roseburia	Roseburia hominis	57.21	3.56	0.06	1.48
7	NR_042817.1	1	1433	1	1427	99.5813	0.995813	35.8	29.0	349741	Bacteria	unclassified Bacteria kingdom	Verrucomicrobiota	Verrucomicrobiia	Verrucomicrobiales	Akkermansiaceae	Akkermansia	Akkermansia muciniphila	1.0	0.06	0.06	0.03
8	NR_043332.1	1	1497	51	1494	99.7996	50.2799	31.0	3.04	479436	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella parvula	50.28	2.89	0.06	1.3
9	NR_044091.1	1	1344	131	1344	100.0	127.859	30.4	41.8	423477	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella rogosae	127.86	3.29	0.03	3.34
10	NR_074784.2	1	1529	3	1483	96.9915	2.85154	29.1	2.67	272559	Bacteria	unclassified Bacteria kingdom	Bacteroidota	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	Bacteroides fragilis	2.85	0.57	0.2	0.08
11	NR_074799.1	1	1534	1	903	58.8657	0.588657	21.0	5.0	90370	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Salmonella	Salmonella enterica	0.59	0.49	0.83	0.03
12	NR_074809.1	1	1535	89	1494	97.329	84.2078	30.2	18.0	585394	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Lachnospirales	Lachnospiraceae	Roseburia	Roseburia hominis	84.21	14.15	0.17	2.27
13	NR_074902.1	1	1542	469	1508	97.7951	448.909	30.5	5.99	585054	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia fergusonii	448.91	71.8	0.16	11.94
14	NR_074980.1	1	1551	30	1525	98.3237	27.3346	26.9	1.43	479436	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella parvula	27.33	4.6	0.17	0.76
15	NR_104826.1	1	1530	253	1491	97.451	244.169	31.0	1.69	624	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Shigella	Shigella sonnei	244.17	39.67	0.16	6.44
16	NR_104901.1	1	1515	46	1484	97.9538	43.7835	31.8	10.9	621	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Shigella	Shigella boydii	43.78	6.5	0.15	1.17
17	NR_104927.1	1	1502	79	1502	100.0	77.4574	32.0	14.0	1613	Bacteria	unclassified Bacteria kingdom	Bacillota	Bacilli	Lactobacillales	Lactobacillaceae	Limosilactobacillus	Limosilactobacillus fermentum	77.46	1.43	0.02	2.01
19	NR_112936.1	1	1490	46	1490	100.0	45.2832	31.1	5.67	817	Bacteria	unclassified Bacteria kingdom	Bacteroidota	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	Bacteroides fragilis	45.28	1.08	0.02	1.17
20	NR_113031.1	1	1524	408	1524	100.0	400.73	30.7	3.04	29466	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella parvula	400.73	11.62	0.03	10.39
21	NR_113099.1	1	1479	59	1479	100.0	57.9797	31.4	59.5	28128	Bacteria	unclassified Bacteria kingdom	Bacteroidota	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella	Prevotella corporis	57.98	1.17	0.02	1.5
22	NR_113132.1	1	1464	231	1464	100.0	227.247	30.1	59.7	1121308	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Peptostreptococcales	Peptostreptococcaceae	Clostridioides	Clostridioides difficile	227.25	4.09	0.02	5.88
23	NR_113335.1	1	1501	13	1501	100.0	12.3857	30.5	5.46	1613	Bacteria	unclassified Bacteria kingdom	Bacillota	Bacilli	Lactobacillales	Lactobacillaceae	Limosilactobacillus	Limosilactobacillus fermentum	12.39	0.85	0.07	0.33
24	NR_113378.1	1	1480	64	1480	100.0	62.6899	30.6	25.7	76859	Bacteria	unclassified Bacteria kingdom	Fusobacteriota	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium	Fusobacterium animalis	62.69	1.33	0.02	1.63
25	NR_113570.1	1	1520	17	1505	99.0132	16.1053	30.2	10.1	1110546	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella tobetsuensis	16.11	1.96	0.12	0.43
26	NR_114042.1	1	1467	4	1467	100.0	3.71915	29.7	0.75	562	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia coli	3.72	0.5	0.13	0.1
27	NR_114079.1	1	1467	1	1261	85.9577	0.859577	27.4	1.0	564	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia fergusonii	0.86	0.35	0.41	0.03
28	NR_115355.1	1	1498	444	1498	100.0	437.727	31.5	6.87	39778	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella dispar	437.73	13.12	0.03	11.31
29	NR_117291.1	1	1441	13	1441	100.0	12.8973	33.4	16.5	997347	Bacteria	unclassified Bacteria kingdom	Fusobacteriota	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium	Fusobacterium animalis	12.9	0.41	0.03	0.33
31	NR_119164.1	1	1436	19	1436	100.0	18.6811	31.7	7.68	817	Bacteria	unclassified Bacteria kingdom	Bacteroidota	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	Bacteroides fragilis	18.68	0.67	0.04	0.48
32	NR_119168.1	1	1513	2	1085	71.7118	1.24917	31.2	1.0	479436	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella parvula	1.25	0.87	0.7	0.05
33	NR_119169.1	1	1513	2	1106	73.0998	1.43093	28.6	1.0	39778	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella dispar	1.43	0.89	0.62	0.05
34	NR_136472.1	1	1504	56	1504	100.0	53.8092	30.4	6.7	1499973	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia marmotae	53.81	2.02	0.04	1.43
35	NR_178280.1	1	1466	500	1465	99.9318	489.591	31.0	15.7	411483	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	Faecalibacterium duncaniae	489.59	27.33	0.06	12.73
36	NR_178798.1	1	1428	1	1422	99.5798	0.995798	34.5	12.0	1441714	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Betaproteobacteria	Burkholderiales	Burkholderiaceae	Paraburkholderia	Paraburkholderia fungorum	1.0	0.06	0.06	0.03
37	NR_178971.1	1	1381	198	1381	100.0	194.332	31.4	10.3	1851427	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	Faecalibacterium butyricigenerans	194.33	14.22	0.07	5.04
38	NR_178972.1	1	1372	4	1369	99.7813	3.3914	31.5	2.75	1851428	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	Faecalibacterium longum	3.39	0.79	0.23	0.1
39	NR_179325.1	1	1469	16	1465	99.7277	15.5827	30.6	3.38	2682456	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella nakazawae	15.58	1.23	0.08	0.41
40	NR_179326.1	1	1400	1	1117	79.7857	0.797857	30.5	34.0	2686067	Bacteria	unclassified Bacteria kingdom	Fusobacteriota	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium	Fusobacterium watanabei	0.8	0.4	0.5	0.03
41	NR_179388.1	1	1472	195	1469	99.7962	191.243	30.8	21.2	2935520	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	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.

index	reference	startpos	ref length	number of reads	covbases	pc coverage	meandepth	meanbaseq	meanmapq	taxid	superkingdom	kingdom	phylum	class	order	family	genus	species	mean	sd	Coefficient of Variance	pcreads
0	NR_024570.1	1	1450	1	1404	96.8276	0.968276	34.3	13.0	562	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia coli	0.97	0.18	0.19	0.03
1	NR_025569.1	1	1494	1	796	53.2798	0.532798	20.8	0.0	208962	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia albertii	0.53	0.5	0.94	0.03
2	NR_026331.1	1	1488	251	1488	100.0	246.319	29.7	7.99	623	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Shigella	Shigella flexneri	246.32	6.18	0.03	6.41
3	NR_026332.1	1	1487	52	1487	100.0	51.271	30.3	45.9	622	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Shigella	Shigella dysenteriae	51.27	1.21	0.02	1.33
4	NR_027549.1	1	1473	21	1473	100.0	20.4372	29.0	5.14	585054	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia fergusonii	20.44	1.66	0.08	0.54
5	NR_028961.1	1	1462	4	1456	99.5896	3.24419	29.9	1.75	853	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	Faecalibacterium prausnitzii	3.24	1.06	0.33	0.1
6	NR_041879.1	1	1375	1	995	72.3636	0.723636	32.8	1.0	39778	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella dispar	0.72	0.45	0.62	0.03
7	NR_042008.1	1	1485	56	1480	99.6633	54.5643	31.2	4.57	585394	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Lachnospirales	Lachnospiraceae	Roseburia	Roseburia hominis	54.56	3.54	0.06	1.43
9	NR_042817.1	1	1433	4	1433	100.0	3.94766	32.1	25.8	349741	Bacteria	unclassified Bacteria kingdom	Verrucomicrobiota	Verrucomicrobiia	Verrucomicrobiales	Akkermansiaceae	Akkermansia	Akkermansia muciniphila	3.95	0.24	0.06	0.1
10	NR_043332.1	1	1497	81	1494	99.7996	79.3721	31.0	2.75	479436	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella parvula	79.37	4.54	0.06	2.07
11	NR_044091.1	1	1344	155	1344	100.0	151.324	30.6	42.4	423477	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella rogosae	151.32	3.34	0.02	3.96
12	NR_074436.1	1	1505	11	1474	97.9402	10.6611	32.5	26.9	239935	Bacteria	unclassified Bacteria kingdom	Verrucomicrobiota	Verrucomicrobiia	Verrucomicrobiales	Akkermansiaceae	Akkermansia	Akkermansia muciniphila	10.66	1.59	0.15	0.28
13	NR_074784.2	1	1529	5	1490	97.4493	4.23349	30.3	3.0	272559	Bacteria	unclassified Bacteria kingdom	Bacteroidota	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	Bacteroides fragilis	4.23	1.08	0.26	0.13
14	NR_074809.1	1	1535	106	1495	97.3941	101.672	30.5	18.8	585394	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Lachnospirales	Lachnospiraceae	Roseburia	Roseburia hominis	101.67	16.8	0.17	2.71
15	NR_074902.1	1	1542	386	1518	98.4436	368.753	30.3	7.65	585054	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia fergusonii	368.75	59.0	0.16	9.86
16	NR_074910.1	1	1544	4	1501	97.215	3.84585	29.5	4.75	90371	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Salmonella	Salmonella enterica	3.85	0.69	0.18	0.1
17	NR_074980.1	1	1551	36	1520	98.0013	33.5338	28.2	1.22	479436	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella parvula	33.53	5.5	0.16	0.92
18	NR_104826.1	1	1530	200	1492	97.5163	192.591	30.8	1.65	624	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Shigella	Shigella sonnei	192.59	31.29	0.16	5.11
19	NR_104901.1	1	1515	31	1484	97.9538	29.8904	31.4	12.7	621	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Shigella	Shigella boydii	29.89	4.41	0.15	0.79
20	NR_104927.1	1	1502	82	1502	100.0	81.2856	31.8	13.8	1613	Bacteria	unclassified Bacteria kingdom	Bacillota	Bacilli	Lactobacillales	Lactobacillaceae	Limosilactobacillus	Limosilactobacillus fermentum	81.29	1.26	0.02	2.1
22	NR_112936.1	1	1490	42	1490	100.0	41.0309	30.5	5.19	817	Bacteria	unclassified Bacteria kingdom	Bacteroidota	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	Bacteroides fragilis	41.03	1.0	0.02	1.07
23	NR_113031.1	1	1524	565	1524	100.0	551.958	30.7	3.1	29466	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella parvula	551.96	15.91	0.03	14.44
24	NR_113099.1	1	1479	73	1479	100.0	72.2218	30.4	59.9	28128	Bacteria	unclassified Bacteria kingdom	Bacteroidota	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella	Prevotella corporis	72.22	1.33	0.02	1.87
25	NR_113132.1	1	1464	230	1464	100.0	224.846	30.2	59.5	1121308	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Peptostreptococcales	Peptostreptococcaceae	Clostridioides	Clostridioides difficile	224.85	4.63	0.02	5.88
26	NR_113335.1	1	1501	14	1501	100.0	13.7382	28.2	3.21	1613	Bacteria	unclassified Bacteria kingdom	Bacillota	Bacilli	Lactobacillales	Lactobacillaceae	Limosilactobacillus	Limosilactobacillus fermentum	13.74	0.62	0.05	0.36
27	NR_113378.1	1	1480	91	1480	100.0	89.7514	30.5	22.9	76859	Bacteria	unclassified Bacteria kingdom	Fusobacteriota	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium	Fusobacterium animalis	89.75	1.52	0.02	2.33
28	NR_113570.1	1	1520	22	1506	99.0789	19.6151	30.4	10.7	1110546	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella tobetsuensis	19.62	3.01	0.15	0.56
29	NR_114042.1	1	1467	8	1462	99.6592	7.81731	28.0	1.38	562	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia coli	7.82	0.69	0.09	0.2
30	NR_114079.1	1	1467	2	1157	78.8684	1.41036	32.1	4.0	564	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia fergusonii	1.41	0.82	0.58	0.05
31	NR_115355.1	1	1498	580	1498	100.0	570.357	31.1	7.58	39778	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella dispar	570.36	17.68	0.03	14.82
32	NR_117291.1	1	1441	20	1441	100.0	19.7953	30.7	10.7	997347	Bacteria	unclassified Bacteria kingdom	Fusobacteriota	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium	Fusobacterium animalis	19.8	0.54	0.03	0.51
33	NR_117759.1	1	1345	3	1343	99.8513	2.93606	27.8	20.7	479436	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella parvula	2.94	0.27	0.09	0.08
34	NR_119164.1	1	1436	11	1436	100.0	10.9088	31.4	15.2	817	Bacteria	unclassified Bacteria kingdom	Bacteroidota	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	Bacteroides fragilis	10.91	0.34	0.03	0.28
35	NR_119168.1	1	1513	3	1040	68.7376	1.87178	31.1	6.33	479436	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella parvula	1.87	1.35	0.72	0.08
36	NR_119169.1	1	1513	2	1101	72.7693	1.42102	32.5	1.0	39778	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella dispar	1.42	0.89	0.63	0.05
37	NR_136472.1	1	1504	53	1504	100.0	52.1031	29.6	4.06	1499973	Bacteria	unclassified Bacteria kingdom	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia marmotae	52.1	1.5	0.03	1.35
38	NR_178280.1	1	1466	347	1465	99.9318	340.012	30.7	16.4	411483	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	Faecalibacterium duncaniae	340.01	18.8	0.06	8.87
39	NR_178971.1	1	1381	142	1378	99.7828	139.553	31.6	11.0	1851427	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	Faecalibacterium butyricigenerans	139.55	9.96	0.07	3.63
40	NR_178972.1	1	1372	1	1342	97.8134	0.978134	31.5	1.0	1851428	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	Faecalibacterium longum	0.98	0.15	0.15	0.03
41	NR_179325.1	1	1469	22	1465	99.7277	21.4786	29.7	5.95	2682456	Bacteria	unclassified Bacteria kingdom	Bacillota	Negativicutes	Veillonellales	Veillonellaceae	Veillonella	Veillonella nakazawae	21.48	1.57	0.07	0.56
42	NR_179326.1	1	1400	1	1397	99.7857	0.997857	35.6	1.0	2686067	Bacteria	unclassified Bacteria kingdom	Fusobacteriota	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium	Fusobacterium watanabei	1.0	0.05	0.05	0.03
43	NR_179388.1	1	1472	191	1470	99.8641	186.253	30.1	20.7	2935520	Bacteria	unclassified Bacteria kingdom	Bacillota	Clostridia	Eubacteriales	Oscillospiraceae	Faecalibacterium	Faecalibacterium hattorii	186.25	10.66	0.06	4.88

Software versions

Name	Version
pysam	0.21.0
pandas	2.0.3
fastcat	0.15.1
minimap2	2.26-r1175
samtools	1.18
taxonkit	v0.15.1
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
bracken_length	None
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_2024-09-01.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_2024-09-01.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