PATHDET v2.0

Version 2.0

Run ID : fastq_202105061233322818260_7bb16b5ea08b630ae3b689782ef1ecd9

Sequence type : Long-read sequence

Specimen Information

Host Type: Homo_sapiens
Specimen Type: Sputum/Throat swab
Patient Status: Onset
Culture Test Result: Positive
Project name: Human Rhinovirus (demo)

Progress Status

1. Processing Start	288509 reads	May06,2021 12:51:22(JST)
2. Quality Check	288509 reads remained	May06,2021 13:38:15(JST)
3. Host Genome Subtract	9227 reads remained	May06,2021 13:47:01(JST)
4. Rapid Pathogen Search	Finished!	May06,2021 13:57:09(JST)
5. Full Pathogen Search	Finished!	May06,2021 16:37:14(JST)

NanoStat

NanoStat

**[1] General summary**
Mean read length	3,666.4
Mean read quality	10.1
Median read length	2,449.0
Median read quality	9.8
Number of reads	288,509.0
Read length N50	5,997.0
STDEV read length	3,801.8
Total bases	1,057,792,997.0

**[2] Top 5 longest reads (mean quality score)**
1:	91328 (10.5)
2:	71664 (7.6)
3:	67298 (9.6)
4:	63106 (9.9)
5:	62640 (9.9)

Rapid Report

[MASH SCREEN LIST (Top 5)] >>What is MASH SCREEN?
identity	microorganisms
0.850067	NC_001490.1 Human rhinovirus 14, complete genome
0.837273	NC_020518.1 Escherichia coli str. K-12 substr. MDS42 DNA, complete genome
0.821262	NC_001781.1 Human respiratory syncytial virus, complete genome
0.818432	NC_018671.1 Sauropus leaf curl disease associated DNA beta, complete genome
0.806739	NC_001782.1 Saccharomyces cerevisiae killer virus M1, complete genome

**[1] Top three hits at family level**
Name	RPM*	RA**
Enterobacteriaceae	5310.06	0.416757
Picornaviridae	3389.84	0.26605
Hominidae	1424.57	0.111807

**[2] Top three hits at genus level**
Name	RPM*	RA**
Escherichia	3920.15	0.327826
Enterovirus	3372.51	0.282029
Homo	1424.57	0.119131

**[3] Top three hits at species level**
Name	RPM*	RA**
Escherichia_coli	3694.86	0.319736
Rhinovirus_B	2377.74	0.205759
Homo_sapiens	1424.57	0.123276

* 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)
4.19093	2.11432737607016714	2.47706564154758182	3.03246977781876178

* 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
N/A	N/A	0	0	0

**[1] Top three hits at family level**
Name	RPM*	RA**
Picornaviridae	5348.18	0.35116
Enterobacteriaceae	5341.25	0.350705
Hominidae	1424.57	0.093537

**[2] Top three hits at genus level**
Name	RPM*	RA**
Enterovirus	5330.85	0.367854
Escherichia	3944.42	0.272184
Homo	1424.57	0.0983021

**[3] Top three hits at species level**
Name	RPM*	RA**
Escherichia_coli	3719.12	0.263766
Rhinovirus_B	2582.24	0.183137
Enterovirus_C	2176.7	0.154375

* 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.