# Raw Data Statistics

Sample | Total Yield | Total reads | GC (%) | Q20 (%) | Q30 (%)
--- | --- | --- | --- | --- | ---

Show Description

Quality of the raw data was assessed to check fidelity of the rawdata. Q20 or Q30 represent portion of the reads having quality equal or higher than 20 or 30 phread score, respectively. Phred score of 20 means the base has 99% accuracy. The reads of which Q20 bases occupy 90% are generally accepted as good quality reads for analysis and it is sure that more higher Q20 or/and Q30 enable to get more accurate analysis results. GC contents represent portion of nucleotide GC and AT. In most cases, GC contents of metagenome samples shows half and half because metagenome samples contain various species. If GC or AT contents are much higher than others, it means that GC or AT rich species occupy majority of the metagenome samples.

- · Total Yield (bp) : Total number of bases sequenced.
- · Total reads : Total number of Reads.
- · GC (%) : GC content.
- · Q20 (%) : Ratio of bases that have phred quality score of over 20.
- · Q30 (%) : Ratio of bases that have phred quality score of over 30.

#### Filtered Data Statistics

Sample | Total Yield | Total reads | GC (%) | Q20 (%) | Q30 (%) | Base Quality Plot
--- | --- | --- | --- | --- | --- | ---

Show Description

The raw data were pre-processed using Trimmomatic which can be used to trim adapter sequences and end-base low quality sequences. Quality of the filtered data was assessed to check fidelity of the filtered data. Q20 or Q30 represent portion of the reads having quality equal or higher than 20 or 30 phread score. Phred score of 20 means the base has 99% accuracy. The reads of which Q20 bases occupy 90% are generally accepted as good quality reads for analysis and it is sure that more higher Q20 or/and Q30 enable to get more accurate analysis results. GC contents represent portion of nucleotide GC and AT. In most cases, GC contents of metagenome samples shows half and half because metagenome samples contain various species. If GC or AT contents are much higher than others, it means that GC or AT rich species occupy majority of the metagenome samples.

- · Total Yield (bp) : Total number of bases sequenced.
- · Total reads : Total number of Reads.
- · GC (%) : GC content.
- · Q20 (%) : Ratio of bases that have phred quality score of over 20.
- · Q30 (%) : Ratio of bases that have phred quality score of over 30.
- · Base Quality Plot : This plot shows the average quality of each base.

#### Total Yield

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#### Q20/Q30 scores of Filtered data

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Show Description

Q20 or Q30 represent portion of the reads having quality equal or higher than 20 or 30 phread score. High Q20 or/and Q30 mean that the raw data have high quality and good enough for further analysis.

#### GC content of Filtered data

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Show Description

GC contents represent portion of nucleotide GC and AT. In most cases, GC contents of metagenome samples shows half and half because metagenome samples contain various species. If GC or AT contents are much higher than others, it means that GC or AT rich species occupy majority of the metagenome samples.

#### Base Quality Plot

Show Description

The base quality plot generated by FastQC was used to check the overall quality of the produced data. This plot shows the range of quailty values at each cycle. The x-axis and y-axis are respectively the number of cycles, and phred quality score. Phred quality score of 20 means 99 % accuracy and reads with quality score over 20 are generally accepted as good quality reads.

- · Yellow box : Interquartile range (25-75 %) of phred score at each cycle.
- · Red line : Median of phred score at each cycle.
- · Blue line : Average of phred score at each cycle.
- · Green background : Good quality.
- · Orange background : Acceptable quality.
- · Red background : Bad quality.