PATHDET v2.0

Version 2.0

Run ID : fastq_202103261034413779341_94b7f45994703bf59cfbd3b22bc5a00f

Sequence type : Short-read sequence

Specimen Information

Host Type: Homo_sapiens
Specimen Type: Plasma
Patient Status: Onset
Culture Test Result: Positive
Project name: S. maltophilia bacteremia (demo)

Progress Status

1. Processing Start	1000000 reads	Mar26,2021 10:35:04(JST)
2. Adapter Removal and Quality Trimming	998955 reads remained	Mar26,2021 10:37:12(JST)
3. Host Genome Subtract	3051 reads remained	Mar26,2021 10:37:43(JST)
4. Rapid Pathogen Search	Finished!	Mar26,2021 10:39:14(JST)
5. Full Pathogen Search	Finished!	Mar26,2021 10:58:03(JST)

Rapid Report

**[1] Top three hits at family level**
Name	RPM*	RA**
Xanthomonadaceae	1850.94	0.923577
Hominidae	34.0356	0.016983
Burkholderiaceae	19.0198	0.00949044

**[2] Top three hits at genus level**
Name	RPM*	RA**
Stenotrophomonas	1828.91	0.920867
Homo	34.0356	0.0171371
Ralstonia	17.0177	0.00856851

**[3] Top three hits at species level**
Name	RPM*	RA**
Stenotrophomonas_maltophilia	1521.59	0.852496
Homo_sapiens	34.0356	0.019069
Stenotrophomonas_sp._WZN-1	26.0272	0.0145822

* RPM: Number of sequencing reads per one million sequencing reads
** RA : Relative abundance of the microorganism

Full Report

[Pathogenicity evaluation metrics (Horiba et al., 2018)]
logRPM	Shannon Index(H ; family)	H (genus)	H (species)
3.42024	0.685265624867603574	0.759693003958451588	1.26213783193911588

TAXONOMY

[Pathogenic microorganisms candidates]
Name	RPM*	RA**
Stenotrophomonas_maltophilia	1926.02	0.812157

* RPM: Number of sequencing reads per one million sequencing reads
** RA : Relative abundance of the microorganism

[Mapping coverage for the representative pathogenic microorganism]
ID	Name	Total length	Coverage percentage	Avg. depth of the mapped regions
GCF_900475405.1	Stenotrophomonas maltophilia	4481118	4.511	1.045

**[1] Top three hits at family level**
Name	RPM*	RA**
Xanthomonadaceae	2312.42	0.894309
Burkholderiaceae	53.0555	0.0205188
Hominidae	34.0356	0.013163

**[2] Top three hits at genus level**
Name	RPM*	RA**
Stenotrophomonas	2289.4	0.890923
Burkholderia	35.0367	0.0136346
Homo	34.0356	0.013245

**[3] Top three hits at species level**
Name	RPM*	RA**
Stenotrophomonas_maltophilia	1926.02	0.812157
Stenotrophomonas_pavanii	35.0366	0.0147741
Burkholderia_sp._CQ001	34.0356	0.014352

* RPM: Number of sequencing reads per one million sequencing reads
** RA : Relative abundance of the microorganism

Citation

Please cite the following URL if you are using PATHDET:

https://pathdet.hgc.jp

Disclaimer

The users are responsible for all risks associated with the use of and the data transfer to PATHDET. PATHDET makes no legal liability for any claims or damages arising from the use of PATHDET.
PATHDET is not responsible for the accuracy, equivalence, and completeness of the analysis results.

Usage Policy

Prior to uploading personal sequencing data to PATHDET, the users must remove the sequence reads derived from the individuals to a level unable to identify the personal information.
The use of personal sequence data for PATHDET should be approved by the institutional review board and by the supervisor of the users’ researches.
PATHDET cannot be used to diagnose, treat, prevent, or alleviate a disease or other condition in man or other animals.
The users are allowed to use PATHDET for academic and non-profit purposes but not commercial purposes.
Users’ personal information (e-mail address) is only used for the announcement of analysis submission and completion.
PATHDET deletes the sequence reads immediately after completion of the analyses and does not use or provide the sequence data for any other purposes.