PATHDET

Version 1.0

Run ID : fastq_201912181715512025345_2a27dac6b172dc79c7c7db7ca8552920

Specimen Information

  • Host Type: Homo_sapiens
  • Specimen Type: Plasma
  • Patient Status: Onset
  • Culture Test Result: Positive
  • Project name: Test01

Progress Status

1. Processing Start 1000000 reads Dec18,2019 17:16:10(JST)
2. Adapter Removal and Quality Trimming 998955 reads remained Dec18,2019 17:18:10(JST)
3. Host Genome Subtract 3051 reads remained Dec18,2019 17:18:50(JST)
4. Rapid Pathogen Search Finished! Dec18,2019 17:20:19(JST)
5. Full Pathogen Search Finished! Dec18,2019 17:55:17(JST)

Rapid Report

[1] Top three hits at family level
NameRPM*RA**
Xanthomonadaceae 1221.28 0.941358
Burkholderiaceae 15.0157 0.011574
Nitrospiraceae 11.0115 0.00848762

[2] Top three hits at genus level
NameRPM*RA**
Stenotrophomonas 1193.25 0.937844
Ralstonia 15.0157 0.0118017
Nitrospira 11.0115 0.00865458

[3] Top three hits at species level
NameRPM*RA**
Stenotrophomonas_maltophilia 853.892 0.807765
Stenotrophomonas_sp._Pemsol 58.0607 0.0549243
Ralstonia_mannitolilytica 15.0157 0.0142046

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

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Full Report

[Pathogenicity Prediction]
logRPMShannon Index(H ; family)H (genus)H (species)
3.41291 0.668798524979681923 0.756741694282221977 1.80734444885524527

TAXONOMY


[Predicted pathogenic microorganisms]
NameRPM*RA**
Stenotrophomonas_maltophilia 1413.48 0.61338
Stenotrophomonas_pavanii 372.389 0.161598
bacterium_M00.F.Ca.ET.163.01.1.1 80.0837 0.0347523

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


[Mapping coverage for the representative pathogenic microorganism]
IDNameTotal lengthCoverage percentageAvg. depth of the mapped regions
GCF_000072485.1 Stenotrophomonas maltophilia K279a 4851126 4.305 1.044

[1] Top three hits at family level
NameRPM*RA**
Xanthomonadaceae 2205.3 0.896257
Burkholderiaceae 63.066 0.0256307
Micrococcaceae 18.0188 0.00732303

[2] Top three hits at genus level
NameRPM*RA**
Stenotrophomonas 2171.27 0.891492
Burkholderia 45.0471 0.0184957
Ralstonia 16.0168 0.00657626

[3] Top three hits at species level
NameRPM*RA**
Stenotrophomonas_maltophilia 1413.48 0.61338
Stenotrophomonas_pavanii 372.389 0.161598
bacterium_M00.F.Ca.ET.163.01.1.1 80.0837 0.0347523

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

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Citation

Please cite the following URL if you are using PATHDET:

https://pathdet.hgc.jp


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